The hominin braid

Much has been said ’round the HBD-osphere, lately, on the age of the Pygmy (and Bushmen?)/everyone else split. Greg Cochran of West Hunter, for example, supports a split around 300,000 years ago–100,000 years before the supposed emergence of “anatomically modern humans” aka AMH aka Homo sapiens sapiens:

A number of varieties of Homo are grouped into the broad category of archaic humans in the period beginning 500,000 years ago (or 500ka). It typically includes Homo neanderthalensis (40ka-300ka), Homo rhodesiensis (125ka-300ka), Homo heidelbergensis (200ka-600ka), and may also include Homo antecessor (800ka-1200ka).^[1] This category is contrasted with anatomically modern humans, which include Homo sapiens sapiens and Homo sapiens idaltu. (source)

According to genetic and fossil evidence, archaic Homo sapiens evolved to anatomically modern humans solely in Africa, between 200,000 and 100,000 years ago, with members of one branch leaving Africa by 60,000 years ago and over time replacing earlier human populations such as Neanderthals and Homo erectus. (source)

The last steps taken by the anatomically modern humans before becoming the current Homo sapiens, known as “behaviourally modern humans“, were taken either abruptly circa 40-50,000 years ago,^[11] or gradually, and led to the achievement of a suite of behavioral and cognitive traits that distinguishes us from merely anatomically modern humans, hominins, and other primates. (source)

Cochran argues:

They’ve managed to sequence a bit of autosomal DNA from the Atapuerca skeletons, about 430,000 years old, confirming that they are on the Neanderthal branch.

Among other things, this supports the slow mutation rate, one compatible with what we see in modern family trios, but also with the fossil record.

This means that the Pygmies, and probably the Bushmen also, split off from the rest of the human race about 300,000 years ago. Call them Paleoafricans.

Personally, I don’t think the Pygmies are that old. Why? Call it intuition; it just seems more likely that they aren’t. Of course, there are a lot of guys out there whose intuition told them those rocks couldn’t possibly be more than 6,000 years old; I recognize that intuition isn’t always a great guide. It’s just the one I’ve got.

( <– Actually, my intuition is based partially on my potentially flawed understanding of Haak’s graph, which I read as indicating that Pygmies split off quite recently.)

The thing about speciation (especially of extinct species we know only from their bones) is that it is not really as exact as we’d like it to be. A lot of people think the standard is “can these animals interbreed?” but dogs, coyotes, and wolves can all interbreed. Humans and Neanderthals interbred; the African forest elephant and African bush elephant were long thought to be the same species because they interbreed in zoos, but have been re-categorized into separate species because in the wild, their ranges don’t overlap and so they wouldn’t interbreed without humans moving them around. And now they’re telling us that the Brontosaurus was a dinosaur after all, but Pluto still isn’t a planet.

This is a tree

The distinction between archaic homo sapiens and homo sapiens sapiens is based partly on morphology (look at those brow ridges!) and partly on the urge to draw a line somewhere. If HSS could interbreed with Neanderthals, from whom they were separated by a good 500,000 years, there’s no doubt we moderns could interbreed with AHS from 200,000 years ago. (There’d be a fertility hit, just as pairings between disparate groups of modern HSS take fertility hits, but probably nothing too major–probably not as bad as an Rh- woman x Rh+ man, which we consider normal.)

bones sported by time

So I don’t think Cochran is being unreasonable. It’s just not what my gut instinct tells me. I’ll be happy to admit I was wrong if I am.

The dominant model of human (and other) evolution has long been the tree (just as we model our own families.) Trees are easy to draw and easy to understand. The only drawback is that it’s not always clear exactly clear where a particular skull should be placed on our trees (or if the skull we have is even representative of their species–the first Neanderthal bones we uncovered actually hailed from an individual who had suffered from arthritis, resulting in decades of misunderstanding of Neanderthal morphology. (Consider, for sympathy, the difficulties of an alien anthropologist if they were handed a modern pygmy skeleton, 4’11”, and a Dinka skeleton, 5’11”, and asked to sort them by species.)

blob chart

What we really have are a bunch of bones, and we try to sort them out by time and place, and see if we can figure out which ones belong to separate species. We do our best given what we have, but it’d be easier if we had a few thousand more ancient hominin bones.

The fact that different “species” can interbreed complicates the tree model, because branches do not normally split off and then fuse with other branches, at least not on real trees. These days, it’s looking more like a lattice model–but this probably overstates the amount of crossing. Aboriginal Australians, for example, were almost completely isolated for about 40,000 years, with (IIRC) only one known instance of genetic introgression that happened about 11,000 years ago when some folks from India washed up on the northern shore. The Native Americans haven’t been as isolated, because there appear to have been multiple waves of people that crossed the Bering Strait or otherwise made it into the Americas, but we are still probably talking about only a handful of groups over the course of 40,000 years.

Trellis model

Still, the mixing is there; as our ability to suss out genetic differences become better, we’re likely to keep turning up new incidences.

So what happens when we get deep into the 200,000 year origins of humanity? I suspect–though I could be completely wrong!–that things near the origins get murkier, not less. The tree model suggests that the original group hominins at the base of the “human” tree would be less genetically diverse than than the scattered spectrum of humanity we have today, but these folks may have had a great deal of genetic diversity among themselves due to having recently mated with other human species (many of which we haven’t even found, yet.) And those species themselves had crossed with other species. For example, we know that Melanesians have a decent chunk of Denisovan DNA (and almost no one outside of Melanesia has this, with a few exceptions,) and the Denisovans show evidence that they had even older DNA introgressed from a previous hominin species they had mated with. So you can imagine the many layers of introgression you could get with a part Melanesian person with some Denisovan with some of this other DNA… As we look back in time toward our own origins, we may see similarly a great variety of very disparate DNA that has, in essence, hitch-hiked down the years from older species, but has nothing to do with the timing of the split of modern groups.

As always, I am speculating.

Updated Tentative map of Neanderthal DNA

Based on my previous tentative map of archaic DNA, plus recent findings, eg Cousins of Neanderthals left DNA in Africa, Scientists Report. As usual, let me emphasize that this is VERY TENTATIVE.

Basically: Everyone outside of Africa has some Neanderthal DNA. It looks like the ancestors of the Melanesians interbred once with Neanderthals; the ancestors of Europeans interbred twice; the ancestors of Asians interbred three times.

Small amounts of Neanderthal DNA also show up in Africa, probably due to back-migration of people from Eurasia.

Denisovan DNA shows up mainly in Melanesians, but I think there is also a very small amount that shows up in south east Asia, some (or something similar) in Tibetans, and possibly a small amount in the Brazilian rainforest.

Now some kind of other archaic DNA has been detected in the Hazda, Sandawe, and Pygmies of Africa.

So Why do Native Americans have so much Neanderthal DNA?

Warning: highly speculative post ahead.

As I mentioned the other day:

Worldwide distribution of B006, (from Yotova et al. “An X-Linked Haplotype of Neandertal Origin Is Present Among All Non-African Populations,” Mol. Biol. Evol. 28 (7), 2011).

SNP PCA from Skoglund & Jakobsson’s “Archaic Human Ancestry in East Asia” (2011)

(Please note that Africans do not have chimpanzee admixture, despite the labeling on the graph–no human group has chimp admixture, because chimps and humans have different #s of chromosomes, so even if you could get a successful cross, the resulting child would be infertile, like a mule. I assume the point of the chimp node is just to represent that which has neither Neanderthal nor Denisovan admixture, though of course there is the possibility of some other form of archaic hominin admixture in Africans.)

So, Native Americans appear to have a ton of Neanderthal DNA. (Relatively speaking.)

Possibilities:

1. It’s all measurement error/convergent evolution/something else other than archaic admixture.

As much as I hate to say it, I still consider this very likely. There is just a ton of stuff that we don’t about the Americas–like how and when people first got here. I’m sticking here with what I think are the most scientifically-supported theories, but a lot of this is still quite disputed. In particular, all of this genetic admixture business is still kind of speculative, and when people start talking about finding admixture in the admixture, either life is totally awesome, or we’re trying too hard.

2. Survival at the Fringes theory

A lot of people seem to look at this data and respond with something like, “But Neanderthals are from Europe, not America!” But this is not a big issue; the Indians are descended from people who passed through Neanderthal-inhabited regions (the Middle East), just like everyone else with Neanderthal DNA. The migration to the Americas took place long after they acquired Neanderthal admixture.

But this doesn’t explain why they have so much of it.

My “concentration on the edge” theory states that when one population is displaced by another population, you end up with a “fringe” of the original population’s traits. Sometimes this fringe results in isolated groups, as the invading population completely surrounds or cuts off a remnant population from their former range.

The Ainu, for example, resemble certain other Oceanin groups, but not their neighbors, the Japanese. I’m speculating here, so don’t take my word for it.

But I have a much better case with the distribution of red hair:

(So far I have found nothing explaining that dot over in Russia.)

Red hair is highly associated with the so-called Celtic fringe. It looks like it’s highly concentrated in Wales, Scotland, and parts of Ireland, but since I know a little history, and I know these aren’t areas of concentration, but just the areas that managed to escape being displaced by Anglo-Saxon invaders, just by virtue of being further away from the south-east coast of Britain.

One can imagine that the isolated dot in the middle of Russia might, at one time, have been connected with the other red-haired regions before other peoples invaded the lands between them and cut them off.

Compare to the map of blond hair:

Blond hair looks like it has been spreading steadily outward from a central source.

So what does this have to do with Neanderthal admixture in Native Americans?

It means that I think the Native Americans may have closer to original levels of Neanderthal admixture, while people in Europe and Asia have lower admixture because they mixed with later waves of people who came from Africa and had no Neanderthal admixture.

3. The Bering Strait selected for Neanderthal admixture

Alternatively, the harsh conditions of life in the Bering Strait–where some scientists think the ancestors of today’s Indians hung out (or “paused”) for thousands of years before the ice sheets opened up to let them through–may have selected for winter adaptations that came from ice-age Neanderthals. I have speculated previously that Type-2 Diabetes may actually be a winter adaptation picked up from Neanderthal DNA; now scientists think this DNA may be responsible for high rates of Type-2 Diabetes in Native Americans.

4. Western diseases selected for Western immune responses

One of the interesting things about the Neanderthal DNA hanging around in people is that it appears to code for certain immune responses. West Hunter recently had a great post (TLRs, PAMPs, and Alley Oop) detailing how they work, but for our purposes, “provide immunity” is sufficient. Austin Whittall suggests that back when smallpox, influenza, measles, and all of the other Western diseases tore through the Native Americans, killing about 90% of them, the guys who had more Neanderthal DNA were more likely to survive because they were more likely to be immune to the same stuff as Europeans. By contrast, those Indians with less Neanderthal DNA may have had less immunity to the European diseases, and so been more likely to die, leaving behind a population of high-Neanderthal DNA people.

5. One thing we can say for sure: if the data’s correct, the peopling of the Americas was more complex than previously thought.

There are four areas of particular interest:

A. The highly Neanderthal area in the Pacific Northwest

B. The highly Denisovan area in Brazil

C. The low-Neanderthal area on the South American coast

D. The low-Neanderthal and low-Denisovan area along the Baja gulf in Mexico.

I’ve got nothing on A and C; supply your own theories.

6. Speculations on the origins of high-Denisovan people in Brazil:

A couple of papers in Science and Nature recently proposed that Melanesian-related people somehow made it to the rain forest long after the other Indians got to the area. West Hunter helpfully summarizes them.

West Hunter suggests that the Melanesian-related people with their high-Denisovan DNA got to the Americas first, and were then replaced throughout the continents by later invaders, the ancestors of current Indians. The one place the Melanesian-related people managed to survive was in the depths of the rainforest, a very difficult place to conquer. Even today, there are “uncontacted tribes” living in the Amazon rainforest; if anywhere were a good spot for a group of humans to avoid getting conquered, the depths of the rainforest is a good one.

7. The low-Neanderthal and low-Denisovan area along the Baja gulf in Mexico.

So what’s up with that? As far as I know, the only people who don’t have any Neanderthal or Denisovan are Africans. (And even there, there’s a little, just due to back-migration from the rest of the world.)

Are these people descended from a totally different group that came directly from Africa?

There’s a tiny ethnic group in the area, called the Seri:

Dona Ramona of the Seri Indians of Sonora, Mexico

According to the Wikipedia, the Seri speak a language isolate–that is, their language, like Basque, doesn’t appear to be related to any other language on Earth–and they are not culturally connected with any of their neighbors. They’ve also held out significantly against Spanish and Mexican assimilation. In other words, they might very well be a totally isolated population that is not related at all to any of their neighbors.

Some more information on the Seris.

Then I found this interesting map:

maps showing global distribution of the HLA-B*73:01 allele

I found these maps over on Austin Whittall’s post on Denisovans and America.

Looks like the same spot, doesn’t it?

The two different “real” maps how different things because they come from different scientists who came up with different data, but the overall picture is similar–if you look closely, both maps show a hotspot in Israel, for example. The second map looks less detailed, (hence their miss of several Middle Eastern hotspots,) but has a wider global range, which is obviously useful for our purposes. They also help show the importance of not putting too much stock in any single study about the distribution of a particular gene or allele or whathaveyou; different scientists come up with different numbers.

At any rate, while this could be just a totally random coincidence, if it isn’t, it’s awfully interesting, isn’t it? I know the Egyptians circumnavigated Africa; the Carthaginians and Phoenicians were also noted sea-farers. Or perhaps some other group I know nothing about from the region, before folks started keeping good records. Who knows?

8. Other people’s theories: Neanderthals, Denisovans, and H erectus made it to America before we did, and H Sapiens intermixed with them after they arrived; humans evolved in American, and then migrated to the rest of the world from there.

Pygmies: Among the world’s most isolated peoples, or archaic hominin admixture?

Pygmies are interesting because:

1. They’re the world’s shortest peoples

2. They’re rainforest hunter-gatherers

3. They appear to have split off from the rest of humanity and have been relatively isolated for longer than almost anyone else on Earth.

4. They’re getting wiped out by their neighbors, so we’d better learn about them now.

First, Who are the Pygmies?

“Pygmy” does not refer (as far as we know) to one specific ethnic group, but to the members of any ethnic group in which adult men are, on average, 4’11” or shorter. In practice, people tend to only use the word Pygmy to refer to certain African groups; there are short-statured groups found outside of Africa, but we’ll discuss them in another post.

The principle African Pygmies are the Aka, Baka, Mbuti, and Twa. (Some countries and groups use different name; I am not an expert on Pygmies, so I’m sure there is much I’ve missed.) The Mbuti are probably the shortest, with an average height under 4’6″. There are about 250,000 to 600,000 Pygmies, scattered about the Congo rainforest:

Locations of some Pygmy groups

We’ve known for a while that the Pygmies–especially the Mbuti Pygmies–and their more southerly neighbors, the San, appear to be the most genetically divergent people on Earth:

Average age of SNPs in different populations, from West Hunter

You might have to squint, but the Pygmies and San are on the far right.

In normal English, what does this mean? Here is my understanding:

There are parts of your (our) genome where random mutations won’t generally kill you. Random mutations tend, therefore, to accumulate there. Since have some pretty decent estimates for how often random mutations occur, comparing the mutations in two different populations lets us estimate how long ago they split. For example, let’s suppose you get one random mutation per hundred years, and we’re comparing two populations that split 300 years ago and haven’t seen each other since. Population A should have gotten 3 mutations during that 300 years, and Population B should have gotten 3 mutations. So if we look at a third population, C, and find that they have 5 mutations that they don’t share with A or B, then we conclude that C split off from some ancestral population 500 years ago. We can reconstruct this as: 600 years ago, there was a group called ABC, but 500 years ago, it split into Group AB and Group C. 300 years ago, Group AB split into Group A and Group B.

Anatomically Modern Humans (that is, Homo Sapiens Sapiens,) according to our best estimates, emerged around 200,000 years ago in central Africa. We’re used to talking about the Out of Africa event, when humans started wandering around the rest of the globe, but it looks like the first major migration event might have been toward the south:

Map of early diversification of modern humans according to mitochondrial population genetics, from Wikipedia

Those guys who went south (Pygmies, Bushmen aka San,) look like they’ve been isolated down there for an awfully long time–much longer than, say, the Australian Aborigines, who got to Australia about 50,000 years ago.

A recent paper by PingHsun Hsieh et al, “Whole genome sequence analyses of Western Central African Pygmy hunter-gatherers reveal a complex demographic history and identify candidate genes under positive natural selection,” describes the results of sequencing 4 Biaka Pygmy genomes and comparing them to 3 Baka Pygmy and 9 Yoruba genomes. (The Yoruba are farmers.)

“Our two best-fit models both suggest ancient divergence between the ancestors of the farmers and Pygmies, 90,000 or 150,000 years ago. We also find that bi-directional asymmetric gene-flow is statistically better supported than a single pulse of unidirectional gene flow from farmers to Pygmies, as previously suggested.”

That’s a long time ago!

(“Bi-directional asymmetric gene-flow” means that they have occasionally inter-married, but not equal numbers of men and women.)

BUT, and this is where I get speculative and may be saying things that a real scientist would tell me are just dumb, what if the Pygmies (and San) actually split off more recently, and just picked up some archaic hominin DNA on their way south?

It’s not so far-fetched an idea. Everyone outside of Sub-Sharan Africa seems to have some Neanderthal DNA, picked up around the time their ancestors left Africa (Northern Africa has had a lot of mixing with non-African populations over the years, so I assume North Africans have Neanderthal DNA, too.) Melanesians (eg, guys from Papua New Guinea and a bunch of tiny Pacific Islands,) and Australian Aborigines are about 4%-6% Denisovan, but it looks like no one else is. Wikipedia article on archaic admixture.

Less is known about potential hominin admixture in Sub-Saharan populations. This may just be because we’ve sequenced far more European genomes and all sorts of remains tend to rot really quickly in the rainforest, making it hard to uncover any archaic DNA to compare modern humans to. However, I can’t help but think that few scientists wanted to be the guy who announced archaic hominin admixture in Sub-Saharan Africans before it was announced in Europeans. That seems like the kind of finding that could quickly get your department defunded, not to mention a lot of people mad at you and a ton of nonsense on the internet.

But with archaic admixture showing up all over the place, no one need worry about the political implications anymore, and science can get on with its business.

So, anyway, what if, on their way into the rainforest, the Pygmies’ ancestors encountered–and bred with–some other group of archaic hominins? (No, not chimps or gorillas–they have a different number of chromosomes than we do, so you couldn’t get viable offspring with them, similar to how mules are infertile.) They would have been more like Neandearthals, though obviously probably shorter.

It seems to me that a more recent divergence from other human groups + archaic admixture could result in a similar number of different genetic mutations as a much more ancient divergence + no admixture.

It also seems like you could have a third scenario: Pygmies (and San) have experienced recent selective pressure on parts of their genomes that no one else has. Maybe the parts of the genome that for everyone else have been just been accumulating random mutations have been important for the recent evolution of the San and Pygmy peoples, and so they’ve been accumulating changes faster than everyone else.

 

At any rate, the Pygmies are still genetically unique among humans.

Unfortunately, the Pygmies are not doing so well. The Batwa got kicked out of their homes in order to make a gorilla reserve. As hunter gatherers with no title deeds to the land they lived on, the government (Uganda) didn’t bother to give them new land or homes. In other words, the Batwa Pygmies were treated worse than the gorillas. (Today, some NGOs have helped the Batwa get new land and set them up as a living ethno-theme park for tourists, which I guess isn’t the worst fate in the world.)

The Bantus (who, despite living in Africa, are probably more closely related to Koreans than Pygmies,) use the Pygmies as slaves.

The Congolese (Democratic Republic of the Congo) have been literally eating the Pygmies, especially the Mbuti Pygmies, whom they regard as sub-human. Astoundingly, one of the reasons cited for genocidal cannibalism is that they want to open up Pygmy lands for mineral exploitation.

70,000 Pygmies have been killed in the civil wars in the DRC and Rwanda.

While I caution against idolizing the Pygmy villages as non-violent Edens (I have no idea what their violence rates are, but past experience suggests that it’s probably actually pretty high,) at least they aren’t cannibals. The Pygmies are smaller than everyone else and have only stone-age technology, so they tend to get defeated easily.

Pretty soon, there might not be any Pygmies left to talk about.

Some photos:

Pygmy village

 

Women of the Batwa Pygmies

 

Batwa Pygmies singing and dancing