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May 21, 2019

Adaptation, the gift of the Denisovans

Filed under: Adaptation,Denisovans,geenetics,Tibet — Razib Khan @ 10:57 pm
The Tibetan Plateau

The city of Lhasa, the capital of the Tibetan Autonomous Region, is at ~12,000 feet above sea level. For comparison, Denver, Colorado, is on average close to ~5,500 feet above sea level. The “Mile High” city has nothing on Lhasa! But believe it or not, Lhasa is in a valley. The average elevation of the Tibetan Plateau as a whole is ~14,500 feet above sea level.

It is not for nothing that Tibet is sometimes called the “roof of the world.”
Potala Palace

The stark and austere beauty of this region has long attracted romantics and inspired legends of lost civilizations and ancient wisdom. Tibetans are known for a unique culture and a hardy people. Over 1,000 years ago a vast region of Central Asia was dominated by the Tibetan Empire. But the Tibetan Plateau itself has rarely been invaded.

Perhaps one reason is a matter of biology: Tibetans are better adapted to high altitudes than their neighbors to the north, south, west, and east. Of course, most people can adapt physiologically in the short-term to a higher elevation, but altitude sickness is the normal response to spending too much time too high up for most humans. In contrast, Tibetans can flourish when others tend to suffer discomfort. Importantly, Tibetan women seem to give birth to healthier and heavier infants at higher elevations than non-Tibetans.

Tibetan Mastiff

Over the past ten years, the genetic basis of Tibetan adaptation to high altitude has been elucidated, and one gene that has come to be as important is EPAS1. One of the names for the protein generated by EPAS1 is “hypoxia-inducible factor-2alpha.” Though most scientific jargon is quite impenetrable, the term “hypoxia” should jump out at you, as that’s the term for oxygen deprivation.

And EPAS1 is not only of interest in the case of adaptation for Tibetans humans. Tibetan Mastiff dogs seem to be adapted to high elevation to due to a mutation in EPAS1 which they absorbed from interbreeding with Tibetan wolves. It turns out that only is the mutation in EPAS1 in these dogs different from other breeds, but the region in the genome in the mutation looks a lot more like Tibetan wolf than dog.

Haplotype network showing Tibetan EPAS1 as distinct

Several years before this, researchers found something similar for EPAS1 in humans in Tibetan when it comes to high altitude adaptation. The paper was titled Altitude adaptation in Tibet caused by introgression of Denisovan-like DNA, and that gives the game away.

Scientists had already known for several years that the EPAS1 region in Tibetans was strange. Far different from other human populations. Where Tibetans and Han Chinese were much more similar to each other genetically than they were to Europeans overall, around EPAS1 Han Chinese and Europeans were much more similar to each other than either were to Tibetans!

In fact, the whole area around the EPAS1 mutation was defined by a set of very distinct markers different from anything researchers saw in other human populations. On a lark, they checked ancient genomes from prehistoric populations, Neanderthals and Denisovans. To their surprise, they found that the Tibetan EPAS1 mutation was surrounded by a region of the genome that matched that from the Altai Denisovans!

The implication from this is that the Tibetans who are adapted to the highlands of their homeland carry a mutation which has very deep roots in this part of Eurasia, as Denisovans occupied it for hundreds of thousands of years. As the first modern humans mixed with these ancient people ~50,000 years ago, they picked up this variation of EPAS1, and modern Tibetans, though descended from migrants from lower elevations within the last 10,000 years, found it fortuitous as they adapted to a high altitude lifestyle.

It turns out that the legacy of the first human people of Eurasia remains with us today, and that legacy can be quite useful. It is one of their gifts to us, their descendents.

Adaptation, the gift of the Denisovans was originally published in Insitome on Medium, where people are continuing the conversation by highlighting and responding to this story.

April 24, 2019

The Insight Show Notes — Season 2, Episode 24: Deconstructing the Denisovans

Filed under: Denisovans,Podcast,science,Uncategorized — Razib Khan @ 2:55 pm

The Insight Show Notes — Season 2, Episode 24: Deconstructing the Denisovans

The Dali skull, 200,000 years old. A Denisovan?

This week on The Insight (Apple Podcasts, Spotify, Stitcher and Google Podcasts) Spencer is back, as we go back to our old two-man show format (at least for this episode). We discuss “deconstruct” the Denisovans, one of the newest human species discovered by science.

The Altai

But before we dug into the paleogenomics, Spencer discussed the human and physical geography of Inner Asia, and in particular the Altai region. In the 1990s Spencer had the opportunity to sample the native peoples of the region, which eventually turned in the Eurasian Heartland paper.

We put the critical role of Inner Asia in a broader historical perspective, from the early Indo-Europeans, down to the Mongols and Turks, and finally the “Great Game” of geopolitical rivalry between Britain and the Russian Empire in the 19th century.

The Altai in many ways has been at the center of Inner Asia. Spencer reflects on the fact that this is where there are Shambhala is often located, a mythical utopian kingdom. While the region is surrounded by cold deserts and forbidding mountains, with the Siberian vastness to the north, the Altai region harbors some relatively sheltered valleys through which nourishing rivers flow.

Inside the Denisova cave

Denisova cave also happens to be in the Altai. This means that not only has the Altai been of historical and mythic importance, but it has been at the center of the understanding of human evolution, and perhaps at the center of human evolution!

We discuss the multiple Denisovan individuals which have been sequenced from the cave. And, the first human ‘hybrid’, a woman whose father was Denisovan, and whose mother was Neanderthal, ‘Denny.’ Denisova cave was inhabited both by Neanderthals and Denisovans, with the Neanderthals having some evidence of modern human admixture, and the Denisovans Neanderthal admixture (and perhaps late Homo erectus).

But the Denisovans were not just a Siberian species. New work suggests there were three deeply distinct Denisovan populations, at least. The people of New Guinea may have had at least three mixing events with Denisovan people, while the admixture in China is almost certainly from a different Denisovan population than that in Oceania.

Finally, we talk about Homo luzonensis, and what the diversity of human across eastern Eurasia means in relation to what it “means to be human.”


The Insight Show Notes — Season 2, Episode 24: Deconstructing the Denisovans was originally published in Insitome on Medium, where people are continuing the conversation by highlighting and responding to this story.

April 23, 2019

Denisovans and the human story

Filed under: Denisovans,Human Evolution,Neanderthals,science — Razib Khan @ 1:38 pm
The Siberian cave where a new human species was discovered

We are all aware of the iconic fossil finds which mark the various milestones of our understanding of human evolution. The story of how our species became what it is today. Raymond Dart’s Taung Child helped establish that Africa might be the original home of our species. Lucy, which put the spotlight on some of the earliest upright ancestors of hominins. Even frauds like Piltdown Man go down in the history books, at least reflecting something of a particular Zeitgeist, wrong as it was.

And yet our past is haunted by a very small collection of remains indeed. Humans were never numerous (until recently). Our ancestors were fossilized thanks to luck, giving us a sense of the shape their form and bearing. The fossil trail of the upright line of apes which eventually lost their fur, and left Africa two million years ago, is quite tenuous.

Denisovan teeth from which DNA was extracted

But in the 21st-century new varieties of humans, species perhaps, are not discovered just by fossils alone. Rather, genetic science has now become adept at retrieving DNA from even the most ancient of human remains. Geneticists can then reconstruct the history of peoples long gone from their sequence, and compare them to modern people or other ancient genomes.

In the spring of 2010, the first whole Neanderthal genome was published, a landmark in the development of paleogenetics. Of course, Neanderthals have a long and storied history in paleoanthropology. They’ve been dehumanized and rehumanized and dehumanized many times. The surprise results out of the Neanderthal genome was that humans outside of Africa were all related to the Neanderthals. In other words, a few percent of the genome of non-Africans could be attributed to descent from them.

But wait! 2010 had more surprises in store for us. At the end of the year, a paper reported the genome of a new species of human. Previously unknown to science, these were the Denisovans, named after the cave in Siberia in which the remains were found. Because there was a genome of Neanderthals already sequenced, scientists could tell that the Denisovans were closer to Neanderthals than to modern humans. About ~750,000 years ago the ancestors of Neanderthals and Denisovans left Africa, separating from our own ancestors. Soon after, the Neanderthals and Denisovans began to diverge, becoming two distinct lineages, far more distinct than any two modern groups.

But why were they distinct?

To answer the question one must look at a map. While Neanderthals occupied Europe and ranged east into the heart of Eurasia, Denisovans likely inhabited the zone between eastern Siberia down into Southeast Asia. Differences develop between populations with common ancestors when they are geographically separated, and by and large (though not exclusively), Denisovans and Neanderthals were separated by the vast arid heart of Eurasia.

While the Neanderthals were a northern population, despite the discovery of Denisovans in a Siberian cave, they may have been used to warmer climes more often than not.

Papuan Woman and Child

One reason this seems likely is that Denisovans have descendants today. But they are not an obscure group in Siberia…they are the Papuans of New Guinea! This population has about ~5 percent of its genome from Denisovans. The descendants of these ancient people are also more widely scattered across Oceania, though to varying degrees.

While the Australian Aboriginals and Negritos of the Philippines have significant Denisovan ancestry, the native tribes of the Andaman Islands have little. This suggests that not all indigenous peoples of South and South Asia mixed equally with Denisovans.

More recent work has revealed that much lower levels of Denisovan ancestry are present across much of South and East Asia. And, importantly, the Denisovan ancestry in groups like the Chinese seems to be from a different group than that mixed into the Papuans. The genome from Denisova cave likely belongs to the people who mixed with East Asians and contributed adaptative functions such as high altitude adaptation in Tibetans.

So what we know now is that for hundreds of thousands of years a widespread group of humans, Denisovans, occupied eastern Eurasia. Unlike Neanderthals, they were not a single homogeneous group. Some research groups have detected three different Denisovan populations mixing into modern humans, while others have suggested that the Denisovans carry ancestry from even earlier hominins, who likely arrived in Asia before them.

But unlike Neanderthals or our African forebears, we have not been able to reconstruct a full skeleton of an individual who is Denisovan.

There are skullcaps, teeth, and stray bones, but not enough identified remains which could give us a sense of what these people looked like, how they were built (though the fragments from Denisova cave indicate to many the Siberian population was robust). Despite what we know was their expansive range, and the fact that they lived in eastern Eurasia for hundreds of thousands of years, to a great extent Denisovans remain genetic ghosts. They are digital shadows of their physical bodies, telling us about their relationships to other humans, details of their physiology, and immune system, but elusive in corporeal form.

The discovery of a new human on the island of Luzon, the existence of hobbits on Flores, and the diversity of Denisovans suggest that the eastern range of humanity during the Pleistocene was filled with many species of humans. The very existence of the Denisovans was window upon the vast ignorance of science in regards to the complexity of the Pleistocene world.

While Neanderthals have been the subjects of many books, they may have been a relatively homogeneous population with very precise adaptations to their northern Eurasian abode. A literal evolutionary sideshow. In contrast, Denisovans ranged from Siberia to the islands of Southeast Asia. From the edge of the tundra to the hot savanna of Sundaland.

They reflect in greater fullness the range of human experience.

Denisovans and the human story was originally published in Insitome on Medium, where people are continuing the conversation by highlighting and responding to this story.

April 19, 2019

The teleos of modern humans

Filed under: Denisovans,Human Evolution — Razib Khan @ 3:15 pm
Credit: Luke Jostins

Next week’s episode of The Insight is going to be on Denisovans. It’s a long one because so much has come out in the last few months on the specific topic, as well as the broader framing issues (e.g., the discovery of a new human species on Luzon).

One of the major points Spencer and I discussed is how important it is to understand general trends in the hominin lineage, that is, humans, before the great expansion ~60,000 years ago. For example, Neanderthals and Denisovans were very different in their paleoecology and biogeography. Neanderthals seem relatively homogeneous (probably due to repeated mass die-offs). In contrast, the “Denisovans” look to have been very deeply diverged within their clade. If the latest work is correct, and some Denisovan lineages split more than 400,000 years ago and persisted down to >100,000 years ago, then the differences between Denisovans may have been considerably greater than between any modern human lineages. For example, the Khoisan diverged from all other humans ~200,000 years ago, and there are possible deeper lineages, but not that much deeper.

Right now what you know about the Denisovans are from genomes in the Altai region. Imagine if we extrapolated to all modern humans from Altaians? It seems entirely likely that the Denisovan lineage was very diverse because it occupied very diverse territory geographically.

But diversity aside, one of the things I like to point out to people, is that there was an overall trend of encephalization among hominins. Neanderthal brains were growing larger too. We need to understand the natural history of all human lineages to understand what happened 60,000 years ago. I am coming to the conclusion that it wasn’t some incredible miracle of a behavioral big bang, but the inevitable outcome of systemic forces in hairless ape evolution that started ~2 million years ago.

The teleos of modern humans

Filed under: Denisovans,Human Evolution — Razib Khan @ 3:15 pm
Credit: Luke Jostins

Next week’s episode of The Insight is going to be on Denisovans. It’s a long one because so much has come out in the last few months on the specific topic, as well as the broader framing issues (e.g., the discovery of a new human species on Luzon).

One of the major points Spencer and I discussed is how important it is to understand general trends in the hominin lineage, that is, humans, before the great expansion ~60,000 years ago. For example, Neanderthals and Denisovans were very different in their paleoecology and biogeography. Neanderthals seem relatively homogeneous (probably due to repeated mass die-offs). In contrast, the “Denisovans” look to have been very deeply diverged within their clade. If the latest work is correct, and some Denisovan lineages split more than 400,000 years ago and persisted down to >100,000 years ago, then the differences between Denisovans may have been considerably greater than between any modern human lineages. For example, the Khoisan diverged from all other humans ~200,000 years ago, and there are possible deeper lineages, but not that much deeper.

Right now what you know about the Denisovans are from genomes in the Altai region. Imagine if we extrapolated to all modern humans from Altaians? It seems entirely likely that the Denisovan lineage was very diverse because it occupied very diverse territory geographically.

But diversity aside, one of the things I like to point out to people, is that there was an overall trend of encephalization among hominins. Neanderthal brains were growing larger too. We need to understand the natural history of all human lineages to understand what happened 60,000 years ago. I am coming to the conclusion that it wasn’t some incredible miracle of a behavioral big bang, but the inevitable outcome of systemic forces in hairless ape evolution that started ~2 million years ago.

April 3, 2019

Denisovans biogeography is very different from Neanderthals

Filed under: Denisovans,Paleoanthropology — Razib Khan @ 8:50 pm


I want to elaborate on my earlier post, Deep Denisovan Population Structure. Though I don’t put much stock in any particular result, including the most recent ones reported at a conference, I think that biogeography tells us a lot about what we should expect in the future.

First, notice that Neanderthals, Denisovans, and European hunter-gatherers have all exhibited evidence of being subject to massive bottlenecks and very low effective population sizes. Things changed in Europe with the arrival of Neolithic farmers, whose higher genetic diversity is in the range of modern people. I think this is indicative of the fact that abiotic factors, climatic shocks, drove down population sizes periodically consistently with all these northern hominins. I’m not saying that population sizes couldn’t get large periodically, but the fact that later Altai Neanderthals are genetically closer to Neanderthals from Croatia than earlier Altai Neanderthals indicate lots of local population extinction. It applied to Neanderthals, it applied to northern Denisovans, and, it applied to northern modern humans. Only with a change in the mode of production were higher long-term population sizes feasible.

But, I do think there was a difference between Neanderthals and Denisovans. As can be seen in the above map: the eastern Eurasian hominins likely had a tropical reservoir. Neanderthals did not. Part of this is due to geography, with the barrier of the Mediterranean, and marginally habitable zones in the Near East. And this factor is probably related to why there is a genetic difference between the Neanderthal meta-population, and the African meta-population, the latter of which may have prevented southward migration of Neanderthals during difficult climatic periods because their niches were too similar.

In contrast, I think the southern range of Denisovans in southeast Asia probably meant they overlapped with other hominins. I don’t think this should be that surprising. Consider that primates are just more speciose in the tropics, and there are apes in Southeast Asia, as well as Africa. One of the reasons that these forest apes survived down to the present is that they are forest apes, who occupy a different niche than modern humans. In the deep past, one can imagine that Homo floresiensis and various late “erectus” populations could have coexisted with Denisovans, who descended from a migration out of Africa ~750,000 years ago (the common Denisovan-Neanderthal model). It was the expansion of modern humans around ~50,000 years ago that was the real game changer in driving all other hominins toward extinction.

Another reason that I believe Denisovans had a southern range is that like African populations, there is evidence in them of very deeply diverged admixture. It doesn’t look like a multi-hominin situation really persisted in northern Eurasia for long. Though Denisova cave was a point of contact between Neanderthals and Denisovans, obviously with Denny, for most of the high latitude range there was one hominin species. If Denisovans have deep diverged admixture, I think that is probably from southern populations which were in contact with small remnant clusters of other hominins.

Finally, I think Browning et al. is pretty persuasive that there were two pulses of Denisovan admixture in eastern Eurasia. The most parsimonious explanation for these results is that Denisovans occupied the Pacific facade, and as humans moved north they interacted with different Denisovan groups from those of the south. The very fact that Denisovan admixture can be ascertained to have been from different deeply structured in modern humans, while the Neanderthal admixture seems very similar to Vindija population from Croatia, points to the reality that these two Eurasian hominin groups had different long-term meta-population dynamics due to their geographic constraints.

March 29, 2019

Deep Denisovan population structure

Filed under: Denisovans,Human Evolution — Razib Khan @ 5:09 pm


The Denisovan session at the American Society of Physical Anthropology meeting was very interesting. In Science Anne Gibbons reports on the findings, Our mysterious cousins—the Denisovans—may have mated with modern humans as recently as 15,000 years ago:

The elusive Denisovans, the extinct cousins of Neanderthals, are known from only the scraps of bone they left in Siberia’s Denisova Cave in Russia and the genetic legacy they bequeathed to living people across Asia. A new study of that legacy in people from New Guinea now suggests that, far from being a single group, these mysterious humans were so diverse that their populations were as distantly related to each other as they were to Neanderthals.

The finding of two Denisovan lineages in Southeast Asia adds to results reported in Cell last year by Sharon Browning of the University of Washington in Seattle and her colleagues. They had suggested that New Guineans had a separate source of Denisovan DNA than people in East Asia, suggesting at least two mixing events.

“I’m skeptical,” added Cosimo Posth of the Max Planck Institute for the Science of Human History in Jena, Germany. He suggests the hints of a late mating could reflect an encounter of previously isolated modern populations rather than of moderns and Denisovans. In this scenario, modern humans mated with Denisovans, then the modern populations diverged, with each branch retaining a different set of Denisovan genes. The moderns then reconnected, mixing the two sets of Denisovan DNA together again.

Here is one thing that I think is important to remember: unlike Western Eurasia parts of Eastern Eurasia were better insulated from extreme climatic events. Neanderthals show strong evidence of repeated die-offs and population expansion so that in general Neanderthal relatedness is more a function of time than location (i.e., Neanderthals tended to go extinct in much of their range periodically, to be repopulated from refuges).

In contrast, the Denisovan range likely went far into Southeast Asia. It is not surprising that this is a highly structured population, with deep lineages. This is exactly what we see in Africa for the same time period. Tropical Southeast Asia is not as extensive as Africa, but it was more expensive during the Pleistocene due to lower sea levels. Hominins with low population densities occupying a huge range of territory almost certainly had developed local lineages and traditions.

As should be clear in the quotes we shouldn’t take these presented results as definitive. But they are suggestive and align well with earlier work that there were several Densiovan admixtures across Eurasia.

December 26, 2011

The sons of Adam: spirit, not blood


Hominin increase in cranial capacity, courtesy of Luke Jostins


A few years ago a statistical geneticist at Cambridge’s Sanger Institute, Luke Jostins, posted the chart above using data from fossils on cranial capacity of hominins (the human lineage). As you can see there was a gradual increase in cranial capacity until ~250,000 years before the present, and then a more rapid increase. I should also note that from what I know about the empirical data, mean human cranial capacity peaked around the Last Glacial Maximum. Our brains have been shrinking, even relative to our body sizes (we’re not as large as we were during the Ice Age). But that’s neither here nor there. In the comments Jostins observes:

The data above includes all known Homo skulls, but none of the results change if you exclude the 24 Neandertals. In fact, you see the same results if you exclude Sapiens but keep Neandertals; the trends are pan-Homo, and aren’t confined to a specific lineage….


In other words: the secular increase in cranial capacity for our lineage extends millions of years back into the past, and also shifts laterally to “side-branches” (with our specific terminal node, H. sapiens sapiens, as a reference). This is why I often contend as an aside that humanity was to some extent inevitable. By humanity I do not mean H. sapiens sapiens, the descendants of a subset of African hominins who flourished ~100,000 years before the present, but intelligent and cultural hominins who would inevitably construct a technological civilization. The parallel trends across the different distinct branches of the hominin family tree which Luke Jostins observed indicated to me that our lineage was not special, but simply first. That is, if African hominins were exterminated by aliens ~100,000 years before the present, at some point something akin to H. sapiens sapiens in creativity and rapidity of cultural production would eventually arise (in all likelihood later, but possibly earlier!).

This does not mean that I think humanity was inevitable upon earth. For most of the history of this planet life was unicellular. I do not find it implausible that life on earth may have reached its “sell by” date due to astronomical events before the emergence of complex organisms (in fact, from what I have heard the end of life is going to occur ~1 billion years into the future due to the persistent increase in the energy output of Sol, not ~4 billion years in the future when Sol turns into a red giant). But, once complex organisms arose it does seem that further complexity was inevitable. This was Richard Dawkins’ case in The Ancestor’s Tale based simply on the descriptive record. But did the emergence of complex organisms necessarily entail the evolution of a technological species? I don’t think so. It took 500 million years for that to occur (it does not seem that coal resources formed hundreds of millions of years ago were tapped before humans). Given enough time obviously a technological species would evolve (e.g., extend the time of evaluation to 1 trillion years), but note that the earth has only ~5 billion years. Homo arrived on the scene in the last 20% of that interval.

Here I am positing at a minimum two not excessively likely or inevitable events over a 5 billion year time span which would lead to a hyper-technological and cultural species:

- The emergence of multicellular life

- The emergence of a lineage with the propensities of Homo

One Homo evolved and expanded outside of Africa I suspect that something of the form of a technological civilization became inevitable n this planet. We see parallelism in our own short post-Pleistocene epoch. Multiple human societies shifted from hunter-gatherers to agriculturalists over the past 10,000 years. The experience of the New World civilizations in particular illustrates that human universal tendencies are real. Not only were “game changing” cultural forms such as agriculture and literacy invented independently during the Holocene, but they were not invented during earlier interglacials (at least in all likelihood).


Khufu, Necho, Augustus and Napoleon

Why not? Well, consider the cultural torpidity of Paleolithic toolkits, which might persist for hundreds of thousands of years! I suspect some of this due to biology. But even over the Holocene we do perceive that cultural change has proceeded at a more rapid clip as time has progressed (i.e., at a minimum cultural change has been accelerating, and it may be that the rate of acceleration itself is increasing!). Consider that the civilization of ancient Egypt spanned at least 2,000 years. Though there are clear differences, the continuity between Old Kingdom Egypt and the last dynasties before the Assyrian and Persian conquests is very obvious to us, and would be obvious to ancient Egyptians. In contrast, 2,000 years separates us from Augustan Rome. The continuities here are clear as well (e.g., the Roman alphabet), but the cultural change is also clear (if you wish to argue that the early modern and modern period are sui generis, the 1,500 year interval from Augustan Rome to the Neo-Classical Renaissance would still be a stark contrast when compared against an ancient Egyptian reference*, despite the latter’s aping of the forms of the former).

So far I have focused on the vertical dimension of time. But there is also the lateral dimension, of cross-fertilization across the branches of the hominin family tree. The admixture of a Neanderthal element into non-Africans has started to become widely accepted recently, thanks to the confluence of archaeology and genomics in the field of ancient DNA. Even if one rejects the viability of Neanderthal admixture, the solution to the conundrum of these results must still entail stepping away from a simple model of recent exclusive origin of humans from a small African population. There are also hints of admixture with other archaic lineages on the Pacific fringe, and within Africa.

Until recently it was common to posit that modern humans, our own lineage, had some special genius which allowed it to sweep the field and extinguish our cousins. The qualitative result of Luke Jostins’ plot was known; that other hominin lineages also exhibited encephalization. In fact, it was a curious fact that Neanderthals on average had larger cranial capacities than anatomically modern humans. But the reality remained that we replaced them, ergo, we must have a special genius. Until the lack of distinction between Neanderthals and modern humans on loci implicated in the necessary (if not sufficient) competency of language that trait was a prime candidate for what made “us” special. But now I put “us” in quotation marks. The data do point to an overwhelming descent from an African or near-African population for non-Africans over the past 100,000 years. But the “archaic admixture” is not trivial. What was they are us, and we have become what they might have been.

For over two centuries there has been a debate in the West between monogenesis and polygenesis. The former is the position that humankind derives from one single pair or population (the former a straightforward recapitulation of the standard Abrahamic model). The latter is the position that different races of humans derive from different proto-humans, or, for the Christian polygenists that only Europeans descent from Adam and Eve (the other races being “non-Adamic”). Echoes of this conflict persist down to the present era. Many of the earlier partisans of “Out of Africa” have claimed that the proponents of multiregionalism were latter-day polygenists (not without total justification in some cases).

But the conflict between monogenism and polygenism is not the appropriate frame for what is being unveiled by reality before our eyes. What we see in the creation of modern humanity is a monogenic base inflected with the flavors of polygenism. Modern humans descend, by and large, from an expansion of an African population over the past 200,000 years. But on the margins there are other strands and filaments of ancestry which tie disparate populations back to lineages which branched off far earlier from the main trunk. At a minimum hundreds of thousands, and perhaps an order of 1 million years, before our own age. Today genomics avails of us the statistical power to extract out these discordant signals from the fluid “Out of Africa” narrative, but I would not be surprised if in the near future we stumble upon more and more “long branches” of less noteworthy quantity. Admixture is likely to be an old and persistent story in the hominin lineage, with only the most recent substantial bouts of separation and hybridization being of notice and curiosity at this moment in time.

What does all this mean? And why have I juxtaposed deep time natural history across the tree of life with inferences of relatively recent paleoanthropology? Let’s start with two propositions:

- Technological civilization, an outward manifestation of radically complex sentience, is not inevitable, though it is probable given certain preconditions (I believe that the existence of Homo increased its probability to ~1.0 over a reasonable time period)

- Radically complex sentience is not the monopoly of a particular exclusive lineage which accrues its genius from a particular specific forebear

John Farrell has pointed out the possible issues that the Roman Catholic church may have with the new model of human origins. But the Catholic church is only but a reflection of more general human strain of thought. Descent-groups, whether real or fictive, loom large in the human imagination. The evolutionary rationale for this is not too hard to explain, but we co-opt the importance of kinship in many different domains. Like evolution, human cultural forms simply take what is already present, and retrofit and modify elements to taste.

So why are humans special? And why do humans have inalienable rights? Many of us may not agree with the proposition that we are the descendants of Adam and Eve, and therefore we were granted the divine grace of eternal souls. But a hint of this logic can be found in the assumptions of many thinkers who do not agree with the propositions of the Roman Catholic church. Recently I listened to Sherry Turkle arguing against a reliance on “robot companions” which are able to exhibit the verisimilitude of human emotions for those who may be lacking in companionship (e.g., the aged and infirm). Though Turkles’ arguments were not without foundation, some of her arguments were of the form that “they are not us, they are not real, we are real. And that matters.” This is certainly true now, but will it always be? Who is this “they” and this “we”? And what does “real” mean? Are emotions a mysterious human quality, which will remain outside of the grasp of those who do not descend from Adam, literal or metaphorical?

If there arises a point where non-human sentience is a reality, do they have the same rights as we? Though the difference is radical in terms of quantity to some extent I think we know the answer: they are human by the way they are, not by the way their ancestors were. The “taint” of admixture with diverse lineages across the present human tree of life has not resulted in an updating of our understanding of human rights. That is because the idea that we are all the children of Adam, or the descendants of mitochondrial Eve, is a post facto justification for our understanding of what the rights of humanity are, adn what humanity is. And what it is is a particular ecological niche, a way of being, not being who descend down in a line of biological relationship from a particular person or persons.

* The cultural fundamentals of Old Kingdom Egypt arguably persisted in a living fossil form in the temple at Philae down to the 6th century A.D.! Therefore, a 3,500 year lineage of literature continuity.

Image credits: all public domain images from Wikpedia

September 5, 2011

Of beasts and men

“There were giants in the earth in those days; and also after that, when the sons of God came in unto the daughters of men, and they bare [children] to them, the same [became] mighty men which [were] of old, men of renown.” - Genesis 6:4 The Pith: Pygmies and Khoisan have admixture from a [...]

June 16, 2011

Massive Neandertal & Denisovan introgression

Update: John Hawks’ lab is working in the same area, and he disagrees with the specific results presented here. Always reminds you to be careful about sexy results presented at conference! (someone should do a study!)

So claimed Peter Parham at a Royal Society meeting last week, Human evolution, migration and history revealed by genetics, immunity and infection. You can actually listen to the talk by pulling down the mp3 file. To get the part about human evolution and introgression, jump to 24 minutes in.

Here is the general sketch: It looks like ~50 percent of the HLA Class I alleles in Europeans derive from Neandertals, ~70-80 percent of HLA Class I alleles in East Asians derive from Denisovans, and that and ~90-95 percent of HLA Class I alleles in Papuans derive from Denisovans. If you recall, ~2.5% of the total genome content of non-Africans seems to be Neandertal, while ~5% of the total genome content of Papuans seems to be Denisovan. The total genome content proportions are rough estimates, there may be some wiggle room in there. But you can see that the HLA allele admixture estimates from these ancient Eurasian lineages is greater by an order ...

December 23, 2010

The paradigm is dead, long live the paradigm!

Mitochondrial DNA and human evolution:

Mitochondrial DNA from 147 people, drawn from five geographic populations have been analysed by restriction mapping. All these mitochondrial DMAs stem from one woman who is postulated to have lived ab7out 200,000 years ago, probably in Africa. All the populations examined except the African population have multiple origins, implying that each area was colonised repeatedly

And so was published in the year 1987 the paper which established in the public’s mind the idea of mitochondrial Eve, which gave rise to a famous cover photo in Newsweek. This also led to the Children of Eve episode on the PBS documentary NOVA. Here is the summary:

NOVA examines a controversial theory that traces our ancestry to a small group of women living in Africa 300,000 years ago.


As Milford Wolpoff has complained it is probably accurate to characterize the documentary as not particularly “fair & balanced.” Mitochondrial Eve may have been controversial, and subsequently plagued by issues of molecular clock calibration as well as spurious interpretations of the cladograms, but the tide of history was on its side, and PBS was telling that story. And the story was not just the primary science, rather, one had to understand the controversy in light of the debates among paleontologists and between paleontologists and molecular biologists. A group of researchers, spearheaded by Chris Stringer argued for the recent origin of modern humans from Africa on the basis of fossils alone. They were challenged by an established school of multiregionalists who argued for deeper roots of modern human populations, which derived from local hominins which diversified after the the migration of H. erectus out of Africa. The argument of the multiregionalists was that selective sweeps across the full range of the human populations gave rise gradually to modern humanity as we know it, a compound of specific ancient local features and trans-population characters which unified us into a broader whole. Stringer and company presented a simpler model where anatomically modern human being arose ~200,000 years ago in Africa, and subsequently expanded to other parts of the world, by and large replacing the local hominin populations. In the multiregionalist telling Neandertals became human beings, while Out of Africa would imply that Neandertals were replaced by human beings.


ResearchBlogging.orgInto this tendentious landscape of bones stepped the molecular biologists. The critical figure here is Allan Wilson, who in the 1970s argued forcefully from molecular clock evidence for a more recent separation of the human and ape lineage than paleontologists had favored. By the 1980s the paleontologists had generally conceded that Wilson et al. were correct. After this victory he put forward the mitochondrial Eve theory with his student Rebecca Cann. Here Wilson was getting involved with an argument about paleontology. From all the material I’ve read Wilson and Cann were confident that their techniques were superior to old fashioned analysis of fossils, a method which Wolpoff defended vociferously on NOVA. People who were not invested in recent human origins often did not know what to make of the debate. To give you a flavor of what was going on in the late 1980s, here’s Richard Leakey in Origins Reconsidered: In Search of What Makes Us Human:

……In the 1970s, I have been more reluctnant than most to accept Wilson and Sarich’s genetic evident in favor of a recent (five million years ago) origin of hominids, so I thought this would be a chance to redress the balance. In thecourse of my talk I mentioned the mitochondrial DNA evidence and indicated that “I was ready to be persuaded by it.” Surrounded as I was by molecular biologists and geneticists, I imagined it would be a wise think to do, and scientifically proper too.

I was therefore more than a little surprised when, in the bar after my talk, several participants, including the conference organizer, Stepehen O’Brien, cornered me and said, “You don’t have to swallow the Mitochondrial Eve line. We don’t.” Steve and his friends proceeded to tell me why they thought the Eve hypothesis was incorrect…Wilson may have miscalculated the rate of the mitochondrial clock, older mitochondria may have been lost by chance, promoted perhaps by occasional crashes in local pouplation size, natural selection may have favored some recent evolved mitochondrial variant, this eliminating the older lineages. Any of these possibilites might erroneously lave the impression of a recently emerged population….

…In February 1990, Milford and a half a dozen like-minded colleagues organized a session at the annual gathering of the American Association for the Advancement of Science, in New Orleans, the goal of which was to “nail this Mitochondrial Eve nonsense.” Speaker after speaker argued for evidence in support of regional continuity and against localized speciation; for alternative interpretations…It was a powerful presentation, and gathered a lot of press, with headlines like “Scientists Attack ‘Eve’ Theory of Human Evolution” and “Man Does not Owe Everything to Eve, Latest Finding Says.” Chris Stringer, who was speaking at a different session of the meeting, described the anti-Eve seminar as “high-powered salesmenship.” One of Milford’s assault team, David Frayer of the University of Kansas, summarized the deep reaction to Wilson’s work: “Fossils are the real evidence.”

In the 1990s Wolpoff came out with a book, Race and Human Evolution: A Fatal Attraction. It outlined a multiregionalist framework for the origin of modern humans, and also presented a wide ranging review of human paleoanthropology past to present, and, to my eyes made the case that the multiregionalists were on the “right side of history.” I was, and remain, a natural history nerd. Especially a natural history nerd of the human species. I devoured books on the topic in the 1980s and 1990s, and saw the slow shift away from multiregionalism toward an Out of Africa model as the orthodoxy, as transmitted by scientific journalists. As I did not have any horse in the race, it was not a matter of concern either way for me, but, I did observe that the disagreements were personal and sometimes politicized. Race and Human Evolution seems to have been written in part to debunk the idea that multiregionalism gave succor to racism. Rather, Wolpoff inverted the narrative, presenting Out of Africa models as genocidal and exterminationist, in contrast to his model of human populations gliding toward sapiency together through gene flow.

The flip side of course is that many people presented Out of Africa as anti-racist par excellence. Anatomically modern humans were portrayed as the latter day Julius Caesar’s of the hominin world. They came, they saw, and they conquered. The chasm between humans and non-humans may have been wide, but the more appealing aspect of the Out of Africa model is that we were the new kids on the block. All non-African humans derived from Africans, who were the reservoirs of our species’ genetic diversity. The dovetailing of implications of the model with the egalitarian ethos of the age was natural. Here is Pat Shipman in 2003, We Are All Africans:

I don’t expect that the subscribers of the Multiregional hypothesis will be waving a white flag of surrender, although they have lost the great majority of their supporters. At least one of the theory’s most ardent proponents, Wolpoff, is still steadfast in defense of the hypothesis he has so long espoused. While it remains possible that new findings will shift the balance in favor of the Multiregional viewpoint, the consilience of such evidence creates a powerful testament. It would take many new fossils and many new genetic studies to resculpt this intellectual landscape.

By and large the arguments which Shipman lays out were persuasive to someone like me who didn’t know much about bones & stones. Though even I knew of some instances of possible continuity, the mtDNA, Y chromosomal lineages, and autosomal results, did seem to roughly line up appropriately. In the battle between paleoanthropologists who saw continuity in the fossils and those who did not, it seemed reasonable to at the time to give the “tiebreaker” to the geneticists who were generating inferences consistent with Out of Africa.


Grendel

With all that said, it has to be stated that paleoanthropologists such as Chris Stringer did not hold necessarily to total replacement of non-Africans. Total replacement may have been the case, but quite often they did qualify that there may have been some admixture and assimilation with the pre-modern substrate. But the paucity of the genetic data pointing to interbreeding between distant lineages (as opposed to a very recent exclusive common ancestry), especially once the Neandertal mtDNA was shown to be an outgroup, seems to have pushed people to the model where modern humans were an entirely different beast which simply wouldn’t have deigned to to have intercourse with the creatures of yore. In The Dawn of Human Culture the paleoanthropologist Richard Klein lays out a scholarly and measured argument for what is close to a maximalist case for the unique and distinctive nature of modern neo-African humanity:

……the simplest and most economic explanation for the “dawn” is that it stemmed from a fortuitous mutation that promoted the fully modern human brain….an acknowledged genetic link between anatomy and behavior in yet earlier people persisted until the emergence of fully modern ones and that the postulated genetic change 50,000 years ago fostered the uniquely modern ability to adapt to a remarkable range of natural and social circumstances with little or no physiological change.

Arguably, the last key neural change promoted the modern capacity for rapidly spoken phonemic language, or for what anthropologists Duane Quiatt and Richard Milo have called “a fully vocal language, phonemicized, syntactical, and infintely open and productive.”

Wolpoff was on to something. Even if the original Out of Africa proponents did not mean to do so, there was a tendency to remove “higher faculties” from the suite of capabilities of the evolutionary “dead ends.” We were H. sapiens sapiens. If we deigned to allow Neandertals to be a branch of our own species, their subspecies was distinctive. They were less than we in the ways in which modern humans were exceptional, and universal.

This orthodoxy probably resulted in a positive feedback loop for the educated public, in which I include myself. The more the Out of Africa model of neo-African human exceptionalism settled into the received wisdom, the more animalized Neandertals and other human lineages became. Naturally a multiregionalist model of continuity became distasteful, because continuity implied a connection between modern humans and subhumans. The fact that the largest cranial capacities in the whole human lineage were sported by Neandertals became a counterintuitive fact, which just went to show that it was quality, not quantity.

When I was a freshman at university I took a biological anthropology course. The instructor threw out a question to the class. He noted that some paleoanthropologists observed a continuity between the skulls of Australian Aborigines and some Southeast Asian erectine populations. Australian Aborigines are a very robust people, and have been less affected by the trend toward gracility which has been the norm over the past 10,000 years for most human populations. In any case, the instructor asked for a show of hands whether such a possibility should even be discussed openly. The solid majority of the class rejected an open discussion. When asked by the instructor why, many of the students who rejected an examination of the thesis argued that such a possibility opened the path to de-humanization, oppression, and was politically too sensitive. Milford Wolpoff had obviously lost the propaganda war. The students did not consider the possibility of multiregionalism where all human populations exhibited continuity, rather, they assumed that continuity hypothesized for Australian Aborigines was specific to them, and so would associate that population with the less human branches of the hominin tree.

Science is a human cultural endeavour. It is about something real, something objective, but we do look through the glass somewhat darkly. The acceptance or rejection of models are contingent upon correspondence to reality and precision of prediction. But the rise and fall of models, and the rate of their rise and fall, may be subject to cultural dynamics. In The Price of Altruism Oren Harman shows how the cultures of Russia and Britain shaped how they viewed the social implications of evolutionary biology. Similarly, Newtonian mechanics and Darwinian evolution may have been retarded in their initial acceptance in France due to reasons of language and national chauvinism.

Not only do scientific theories have to swim through the waters of suspicion and incomprehension across societies, but they also have to overcome the inevitable confounding of their natural inferences with normative ones. Newtonian mechanics, relativity, and quantum mechanics, have all had many peculiar and surprising downstream social consequences. The line made between these physical theories and models and sociology, epistemology, and spirituality, would likely have surprised their originators (OK, perhaps not Isaac Newton). But the human imagination is fertile, and many cognitive anthropologists argue that the connections and analogies that we make, in addition to our promiscuous pattern recognition, gives rise the baroque and baffling complexity that is culture.

By the mid-2000s the paradigm of Out of Africa had crystallized to such a point that even the fossils purportedly betrayed the multiregionalists. In Bones, Stones and Molecules: “Out of Africa” and Human Origins the authors made the case that the fossil record, and its pattern of variation, complemented the molecular record. That is, Chris Stringer was right. Other more computationally intensive analyses of morphological variation reportedly tended to support an Out of Africa model.

And yet just as Out of Africa seemed to have cleared the field, pointers in the other direction were bubbling up out of genomics and genetics. In 2006 Bruce Lahn at the University of Chicago published Evidence that the adaptive allele of the brain size gene microcephalin introgressed into Homo sapiens from an archaic Homo lineage. Nevertheless several years later there seems to have been no wide support for this hypothesis. For eample, No evidence of a Neanderthal contribution to modern human diversity. But there were other papers nonetheless. Deep Haplotype Divergence and Long-Range Linkage Disequilibrium at Xp21.1 Provide Evidence That Humans Descend From a Structured Ancestral Population. Genomics refutes an exclusively African origin of humans. Granted, this was a minority perspective. For the first few years the Neandertal genome project did not seem to support any admixture either. I saw Svante Paabo speak in late 20008, and he was absolutely unequivocal. No sign of admixture. Period.

But the equilibrium of scientific orthodoxy is not eternally robust to a hard exogenous shock of falsification. Yes, some scientists remain obstinate in the face of overwhelming evidence. One could argue Milford Wolpoff could be numbered amongst these. Fred Hoyle certainly was. But the tide turns. In the fall of 2009 Svante Paabo seemed to be far less unequivocal about the issue of admixture. Then, in the spring of 2010:

A test of the New Mexico team’s proposals may come soon. Svante Pääbo and colleagues at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, announced early last year that they had finished sequencing a first draft of the Neanderthal genome, and they are expected to publish their work in the near future. Pääbo’s earlier studies on components of Neanderthal genomes largely ruled out interbreeding, but they were not based on more comprehensive analyses of the complete genome.

Linda Vigilant, an anthropologist at the Planck Institute, found Joyce’s talk a convincing answer to “subtle deviations” noticed in genetic variation in the Pacific region.

“This information is really helpful,” says Vigilant. “And it’s cool.”

By this point, in April of 2010, some graduate students who were not involved in the project itself had seen hard copy drafts of the Neandertal admixture paper. Word was spreading. I already knew of its likely probability, which resulted in me turning on Google Alerts (which got me in trouble for “breaking embargo” on an embargo which I was never privy to). The hammer-blows against the old tried & true orthodoxy in 2010 were ripening throughout the year, and many people were “in the know.” In the age of transparency it is interesting that science naturally has a culture of some secrecy. Who wants to be scooped? But how sustainable is this really over the long term?

To use a religious analogy which some may find offensive, this was an instance where the heretics were once the high priests of the faith. The media reports from last spring made it clear that most of the principals involved did not initially believe that admixture had occurred. Rather, they assumed that the results they were getting were anomalies. Science is influenced by culture, but ultimately nature remains the final arbiter. The truth is what it is, and honest men and women give it its due.

At this point you presumably know the score. Ancient DNA is a powerful judge and jury. It seems that the evidence for Neandertal admixture is already modifying the conventional Out of Africa narrative. But, it has to be admitted that Out of Africa is predominantly correct. The vast majority of our total genome content seems to be traceable to African populations within the last ~100,000 years. An older model of deep rooted lineages only periodically punctuated by selective sweeps which maintain species cohesiveness is not tenable. Phyletic gradualism seems implausible in light of the genetic evidence. Here is Wolpoff (and his wife, Rachel Caspari) in Race and Human Evolution:

We agree a punctuated evolutionary pattern best describes the evolutionary histories of many phyletic groups, including, we think, the earlier and much longer part of human prehistory when humans were only another African primate species. But we believe punctuated equilibrium does not reflect what happened to humans in the later part of human evolution as they became successful colonizers and when there was no macroevolutionary change. As we read the fossil record, there is no evidence of speciation events in the recent past; in fact, there is strong evidence against them. But the Eve interpretation promised to support a punctuated model for later human evolution that was denied by interpretations of the fossil evidence such as ours.

I’m not knowledgeable enough to know what would qualify as a “macroevolutionary change.” But the ‘Great Leap Forward’ seems a plausible candidate. Whatever the details, between 200 and 10 thousand years ago, there does seem to have been a series of rapid expansions of the human range and capacity for innovation. Sometime different was in the air. I do not know the nuance of Milford Wolpoff’s thinking. The most recent data do seem to refute the contention that all ancestry but the Out of African is trivial. But, they also seem to be broadly in line with the peculiarity, almost revolutionary character, of the changes in the human lineage over the past 200,000 years. Convergent patterns of morphological and genetic variation which seem to root back to an African base indicate that Chris Stringer and Allan Wilson had properly characterized a major first order dynamic in recent human prehistory. But now we move into the second and third orders. The rough paradigm is getting sculpted into something with more verisimilitude when judged against the diversity and peculiarity of nature.

Let’s jump to the paper. The main course. Genetic history of an archaic hominin group from Denisova Cave in Siberia:

Using DNA extracted from a finger bone found in Denisova Cave in southern Siberia, we have sequenced the genome of an archaic hominin to about 1.9-fold coverage. This individual is from a group that shares a common origin with Neanderthals. This population was not involved in the putative gene flow from Neanderthals into Eurasians; however, the data suggest that it contributed 4–6% of its genetic material to the genomes of present-day Melanesians. We designate this hominin population ‘Denisovans’ and suggest that it may have been widespread in Asia during the Late Pleistocene epoch. A tooth found in Denisova Cave carries a mitochondrial genome highly similar to that of the finger bone. This tooth shares no derived morphological features with Neanderthals or modern humans, further indicating that Denisovans have an evolutionary history distinct from Neanderthals and modern humans.

John Hawks has covered a great deal of ground in his FAQ. In particular, he has a gestalt understanding of the fossil record so he can run “quick & dirty” checks on some of their assertions. He notes:

What the paper doesn’t point out is that there are Upper Paleolithic specimens that equal or exceed this tooth in size. For example, the measured length and breadth of an upper second molar from Oase, Romania, are larger than this specimen, and the third molar (in the crypt) of that specimen is yet larger. There is an Upper Paleolithic-associated molar from Turkey which is also exceedingly large.

I don’t take that as a sign of relationship between this specimen and early Upper Paleolithic people — even though these are some of the earliest. It is another sign of how non-diagnostic this tooth actually is. I would say that in the absence of genetic information, we’d be looking at these remains as likely early Upper Paleolithic people, and accentuating these similarities.

People interpret information in light of their background priors. Now that we know what we did not, it may behoove us to go back and double check we may once have dismissed. Consider this paper from 2006, Archaic admixture in the human genome:

One of the enduring questions in the evolution of our species surrounds the fate of ‘archaic’ forms of Homo. Did Neanderthals go extinct without interbreeding with modern humans 25–40 thousand years ago or are their genes present among modern-day Europeans? Recent work suggests that Neanderthals and an as yet unidentified archaic African population contributed to at least 5% of the modern European and West African gene pools, respectively. Extensive sequencing of Neanderthal and other archaic human nuclear DNA has the potential to answer this question definitively within the next few years.

5% is a nice round number. They could have lucked upon it, but the first author continued to plunge onward in 2009, generating models of archaic admixture. How fruitful would this be? Here is Sarah Tishkoff in December of 2009:

…Sarah Tishkoff, a geneticist at the University of Pennsylvania, agrees, adding that, after all, every population has a strong selective pressure for intelligence, the better to succeed in its respective environment. As far as consorting with Neanderthals, Tishkoff dismisses that notion as pure speculation: “I don’t know of any evidence for that.”

I suspect that Sarah Tishkoff’s opinion would have been common among most scholars of human evolution in late 2009 (though I suspect those who were Facebook friends with people in Svante Paabo’s lab perhaps not). To be fair to Tishkoff, she had no compunction about accepting Neandertal admixture six months later when presented with evidence. She even added that “…it is possible that interbreeding introduced traits into a few human populations.”

In regards to the paper, the top line is rather clear in the three figures in the article proper. I’ve reformatted them a bit below:

Top left: a phylogenetic tree which shows the total genome relationship of various human lineages. Extant modern humans represent one clade. The Denisovans and Neandertals another. In other words, the last common ancestral population of Denisovans and Neandertals is shallower in time than the last common ancestral population of neo-Africans and the Denisovans and Neandertals. All the Neandertals also are very closely related, at least when graded on this particular curve. The Denisovans are outgroups to them, just as the San are outgroups to other humans. The French are an outgroup to the Han and Papuans, though just barely. This sort of relationship is naturally why I cast a skeptical eye to arguments of the common ancestry of French and Han 20,000 years ago when we know that the Papuans settled their island 45,000 years ago.

Top right: a PCA where HGDP populations are projected onto the two largest components of variation which shake out of a data set of a chimpanzee, Denisovan, and Neandertal. In other words, the ones deciding the rules of the game here are chimps and the two archaic Eurasian populations. Humans are constrained onto the genetic variation space of non-/pre-humans. So the position of the humans tells you how they relate to the genetic variation of the Denisovans, Neandertals, and chimpanzees. The Eurasicans, Eurasians + Amerindians, form a relatively tight cluster, apart from Africans. If non-Africans have some Neandertal admixture, this is reasonable. But interestingly the Melanesian groups stand apart as well. And, Papuans and Bougainville Islanders are also distinctive. The latter are shifted toward Eurasicans. Why? Probably because they have a minor, but significant, Austronesian ancestral component which the Papuans lack.

They estimate that 2.5% of the genes of Eurasicans and Oceanians is of Neandertal origin. And, a further 5% of the Melanesian genome is of Denisovan origin. So Melanesians are 92.5% neo-African. Eurasicans are 97.25% neo-African. At most.

Bottom: the last shows a stylized demographic model. Step 1, humans leave Africa. The neo-Africans interbreed with southwest Asian Neandertals. Step 2, the paleo-Eurasians push east, and some encounter the Denisovans, eventually reaching Sahul ~45,000 years ago.

Some people have asked me about the Denisovan in Polynesians and Australian Aborigines. Since Polynesians are ~20% Melanesian, they should have a fraction diluted appropriately. As for Australians, if they are only recently distinguished from the peoples of Papua because of rising sea levels I assume that they should carry the same fraction of Denisovan. Bougainville has always been isolated from Papua by water from what I know. A final question is in regards to Andaman Islanders and other isolated Asian peoples who seem to be hunter-gatherer relics such as the Ainu. Since the Pakistani HGDP populations share a large minor component of ancestry with the Andaman Islanders my assumption is that they should be somewhat deviated toward the Papuans. As the populations are not labeled I do not know if those groups are skewed toward the direction of the Papuans. In the supplements individual outcomes are given for the Han and French, and the Han seem somewhat shifted toward the Bougainville Islanders, though trivially. Additionally, some of the authors of this paper were involved in Reconstructing Indian History, and so I assume had access to Andaman Islander data. I would be curious if they ran some quick checks and decided to stick with the HGDP because there was unlikely to be anything there.

The main body of the paper is tightly and elegantly written. But there is so much more in the supplements. I have read through them at least once, but I can’t say I understand it very well. It is written with the tight economy of a mathematically minded individual, despite the fact that it runs to 90 pages. But much of it alludes to a “D-statistic” which actually goes back to the earlier Neandertal admixture paper, and its supplement. So let’s go back to that, and review the D-statistic at least cursorily. One might not gain a deep knowledge, but even a superficial knowledge of the technical arcana of these sorts of papers are often useful in my experience. To page 130:

To test whether Neandertals share more alleles with some present-day human populations than with others, we compared the Neandertal sequence that we generated to sequence from present-day human samples of diverse ancestry. Specifically, we discovered single nucleotide polymorphisms (SNPs) by comparing exactly two chromosomes from different individuals (H1 and H2). We then assessed whether a test individual (H3, e.g. Neandertal) tended to match either H1 or H2 more often at sites where H3 has the derived allele relative to chimpanzee. Under the null hypothesis that H3 belongs to an outgroup population, it should match H1 and H2 equally often. In contrast, if gene flow has occurred, H3 may match one more than the other.

Here’s a graphical illustration:

The ancestral state is A, which the chimpanzee (not shown as H4) presumably has. B represents the derived state. That means it has changed via mutation from the ancestral state at some point from the last common ancestor with the outgroup. To calculate the D-statistic you are looking at a case where H3 is B and H4 is naturally A. So you have two sets: BABA and ABBA. You are comparing the counts between these two combinations. If H3 is a clean outgroup to the H1H2 clade, D will be ~ 0, as BABA and ABBA counts will approximately be equal. In contrast, if there is gene flow to H1 or H2 from H3, D will deviate from ~0. The Z-score are the standard deviations away from ~0. The table below is from the current paper under consideration. I have highlighted and reformatted:

The D-statistics make sense of what you know verbally. There is some admixture from Neandertals to Eurisicans + Oceanians. Therefore when paired with each other as H1 and H2 they do not deviate as from 0 as much as they do when paired with Africans. There is a deviation away from equal ratios of ABBA and BABA because there is putative gene flow from from H3 to H1 or H2. Notice the Denisovans. Because they’re like Neandertals they produce some elevated deviation from D, though not as much. Interestingly the maximum Z-scores occur when comparing Denisovans, Melanesians, and Africans. Finally, Melanesians and Eurasicans also result in a deviation from 0 when paired with Denisovans in the H3 position.

A quick note from the supplements on ancient population structure. Dienekes does not believe that there was Neandertal admixture necessarily among Eurasicans and Oceanians. From what I can gather he believes that there was population structure within Africa, which is preserved in non-African populations. Rather than exogenous admixture between geographically separated lineages which had only recently met, what one is presumably arguing for here is that there were long term barriers between more closely placed populations in Africa. The authors do not find it parsimonious, though they can not reject it as totally without foundation. Below is a graphical representation of their two models:

So where does this leave us? Yesterday when I said something big was going to drop Ed Brayton expressed some frustration that paleoanthropologists tend to hype stories too much. The reality is everything doesn’t change. The Hobbits, the Darwinius fiasco, and the persistent controversy over Ida, can give anyone fits of human evolution fatigue. But there is a difference here. You don’t need to take their total word for it. At some point you will be able to go to the UCSC genome browser and poke around yourself. Or, you can pull down a 153 MB file with SNPs and indels.

This is a great time to be alive if you’re a hominin natural history nerd. You never know what surprise will greet you when you wake up in the morning. You never know how you’ll have to rearrange your conception of the world. Earlier in the post I mentioned that an instructor once asked a class where I was a student whether scientists should be allowed to talk about the erectine features of Aborigines, if they believed such features existed. You probably won’t be surprised that I said that such things shouldn’t be off limits if they seemed true. Obviously science has political implications. It is idealistic and philosophically consistent to say that it is value-free, but it is also naive. Rather, we need to think hard about how our values relate to the world around us. Or at least some of us need to think hard about that sort of thing.

We shouldn’t take for granted that we all have exactly the same moral intuitions. But on the margin some of our fears are I think overwrought. I know of an individual who admits frankly that they are a “blank slate” maximalist because they don’t know how they could sleep or live if many traits had some hereditary component. Similarly, I have met many conservative Christians and Muslims who admit that they would rape, murder and steal if they didn’t believe in God. In other words, if God doesn’t exist they would become psychopaths, because “why not.” This is ludicrous. God doesn’t exist, and they aren’t psychopaths. They may believe that they aren’t sodomizing their sister because the Lord God declared from On High believes that such behavior is forbidden, but I think that’s ridiculous on the face of it (on the margin there may be some effect of belief in God on behavior by the way, but that’s not what I’m getting at here obviously). Everything may be possible, but everything is not palatable. As for the possibility that humans may differ substantially from individual to individual and group to group, if you acknowledge this one day will you then as a matter of course raise in your arms in salute? If so, it is true that humans differ profoundly in matters of moral sense, because I could not comprehend such behavior.

So Papuans, and likely Aborigines, are likely ~7.5% non-neo-African. Does that matter? Do they bleed today where yesterday they did not? In deep matters of substance nothing is different from this moment than before. Let me quote John Hawks:

Our common ancestry as humans goes back to the Early and Middle Pleistocene. The (now multiple) Neandertal genomes and the Denisova genome share genes with some people and not others because of this common ancestry.

In addition, some living people carry even more genes from Neandertals because they have an appreciable fraction of Neandertal ancestry. That makes it nonsensical to talk about “Neandertals and the ancestors of modern humans”. Neandertals are among the ancestors of modern humans.

Just so with Denisova. It’s nonsensical to talk about a three-way split between Neandertals, Denisova and modern humans. We can talk about a population model with a clade separating an ancestral Neandertal-Denisova population from contemporary Africans.

I have to remind myself again and again when I talk to people about these issues that “modern human ancestors” is not a group that excludes these Pleistocene people.

Once we put ourselves into the mode where we are referring to a population model, it is important to recognize the limitations of those models. For example, we cannot presently exclude many kinds of gene flow among these Pleistocene populations. We can understand some limits to the level of gene flow — these populations were highly structured, it wasn’t Pleistocene panmixia. But it is premature to talk about isolation without recognizing the limits of our ability to test these population models.

The difficulty with terminology tells us something very important. A large-scale reorganization of the science of human origins is upon us. The terms we are used to using will, many of them, become obsolete. Some now-obscure terms will become very important.

What we know to be good and true is still good and true. It is a small soul who is so moved by matters of terminology, we should be cautious of allowing that to happen to ourselves. I think now to the fact that both the Romans and Muslims abhorred the idea of the king. The Romans overthrew their monarchy, established a republic, and replaced it with a despotism which was a monarchy in all but name. The Muslims had caliphs, vice-reagents of God, and sultans and emirs, who were vice-reagents of the caliphs. Despite the glory which is given over to their God the Muslim despotisms were things of men. Domination of the many by one is a matter of substance, not style. Human dignity should not be contingent on details of ancestry. Isn’t that obvious? I thought that was what the 20th century was to some extent all about.

Back to the science. I began with a long historical sketch, viewed through my own personal lens, because probabilities are always filtered through a glass of accreted priors. I was not as shocked by many at the idea of intogression and admixture because Greg Cochran, Henry Harpending, and John Hawks had already predisposed me to think about the plausibility of such phenomena. Additionally, I have always had an interest in conservation genetics, as well as modeling cultural evolution. Such lateral flows are not unknown in those domains. When I first discussed the Neandertal admixture results with Oren Harman last spring he reminded me that one should be cautious of such things; many splashy science stories often don’t pan out. And yet with all due respect to Oren, in this case we do need to observe that there has been a veritable mob of scholars pouring over these data. Additionally, this is something old, not something new.

These results will not remain isolated findings with only parochial relevance. I believe these two papers will probably shift the equilibrium orthodoxy in a new direction. Old models and genetic studies will be seen in a new light. Anomalies unconsidered will get a second look. In The New York Times Stanford geneticist Carlos Bustamante seemed to indicate to Carl Zimmer that the hunt was on. Perhaps the human genome is more of a mosaic than we thought?

Finally, one wonders how this was missed. 7.5% is not trivial. And yet a generation of mtDNA and NRY studies have seemingly missed this. I presume that the archaic admixture didn’t show up in STRUCTURE because it’s a stabilized part of the genetic background of Eurasicans and Oceanians. It reminds of us the limitations of interpretation. We know what we know contingent on what we already know. Since we know more, a different set of inferences may now be generated. Though with due humility. Not quite time yet for the hardening of a new orthodoxy.

Personal note: Merry Christmas! Obviously it is time for me to take a break. Best wishes, and let’s make 2011 more informative and data rich. Hopefully we won’t have to wait too long for Otzi’s genome.

Citation: Reich, David, Green, Richard E., Kircher, Martin, Krause, Johannes, Patterson, Nick, Durand, Eric Y., Viola, Bence, Briggs, Adrian W., Stenzel, Udo, Johnson, Philip L. F., Maricic, Tomislav, Good, Jeffrey M., Marques-Bonet, Tomas, Alkan, Can, Fu, Qiaomei, Mallick, Swapan, Li, Heng, Meyer, Matthias, Eichler, Evan E., Stoneking, Mark, Richards, Michael, Talamo, Sahra, Shunkov, Michael V., Derevianko, Anatoli P., Hublin, Jean-Jacques, Kelso, Janet, Slatkin, Montgomery, & Paabo, Svante (2010). Genetic history of an archaic hominin group from Denisova Cave in Siberia Nature : 10.1038/nature09710

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