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.

Tentative map of Neanderthal (and Denisovan) DNA in humans

I couldn’t find one, so I made one:

This is really tentative! And I am not a geneticist, so at this point, I’m just crossing my fingers and hoping I didn’t read any graphs backwards.

Notes:

This map shows Neanderthal DNA admixture in modern human groups (solid color) and Denisovan DNA (polka dots.) The Denisovan estimates are less exact than the Neanderthal estimates. (Also, the guys with Denisovan DNA also have Neanderthal DNA; I just don’t know how much.)

The biggest problem I ran up against was a total lack of numbers. Seriously, everyone likes quoting that “1-4% of non-African DNA is Neanderthal” stat, but no one likes breaking it down by individual country or group.

Some of the sources contradict each other–first we have papers claiming that Europeans have more Neanderthal DNA than Asians, then papers claiming that Asians have more. I went with the Asians have more estimates, since they were more recent. Also, we now think that many African groups also have some Neanderthal DNA, due to more recent back-migration of Eurasians into Africa.

Most of this map is still completely blank, even though I’m sure the data is out there somewhere. I would really appreciate if any of my readers can point me toward a good old list of Neanderthal (or Denisovan) DNA %s by country or group.

Alternatively, if you’ve had your DNA analyzed and know your Neanderthal and/or Denisovan %s, feel free to share in the comments.

When I have more data, I’ll update the map.

Sources read:

Dienekes: Neandertal admixture in modern humans

John Hawks: Neandertal ancestry iced, Neandertal introgression 1,000 genomes style

The Atlantic: The Other Neanderthal

1000 Genomes: about

Wang et al, Apparent Variation in Neanderthal Admixture among African Populations is Consistent with Gene Flow from Non-African Populations

 

 

 

 

 

 

Please, please let me know if you find some better lists of the %s of Neanderthal and Denisovan DNA in different populations.

Review: Decoding Neanderthals on PBS (Nova)

Available on Netflix, maybe elsewhere.

Overall: Recommended if you like Neanderthals or human ancestry. Probably not useful if you are already an expert in the field.

Pros: interesting discussion of flint-knapping, gluey pitch production, and Neanderthal burials.

Flint knapping is one of my occasional interests. It is surprisingly difficult to just pick up a rock and produce a useful tool. Without a good teacher, you quickly degenerate to banging the rock on the ground as hard as you can like a retarded monkey. If Kanzi the bonobo saw me trying to make stone tools, he’d probably bring me some fruit out of pity. “Poor hairless idiot ape,” Kanzi would think. “Can’t even make tools. If I don’t feed it, it’ll starve.”

Amusing digression time: Once I was walking through the city, in a semi-developed/semi-overgrown lot, and saw a bit of shiny rocks lying around on the ground. Unusual for the area, because the local geographic history hasn’t led to a lot of rocks on the surface, and most of those are of the duller sedimentary sorts (or, obviously, landscaping materials.) So I picked up this bit of flint, then another bit of flint, and then a larger one with obvious convex areas from being struck with another piece. And a few feet away, here was a piece that fit comfortably into my hand, perfect for knocking chips off the other chunk. Some of the pieces I even managed to fit back together, reassembling the rock that once was.

I came back with a small box and picked up all the bits of flint before development began on the lot. One piece does look like an arrowhead, but given that I found it alongside a bunch of chips that are more or less flint-knapping trash, the arrowhead’s creator probably thought there was something wrong with it.

Sure, the whole little box may be filled with little more than ancient trash, there is something I love about picking up these rocks and being able to see in their shapes the actions of some other humans, the angle they held that rock at, the way they smacked it with another rock to produce these flakes. To feel this connection between myself and some other human who walked here before me, and the traces of their life that no one else walking through that place had noticed.

Anyway, turns out the Neanderthals had a pretty interesting/unique way of making flint tools, that involved first shaping a large block of flint into a specific shape by flaking bits off the sides, and then, with one good hit, knocking off one large slice. This is a more complicated process than merely picking up a rock and whacking bits off of it it until you get an edge.

The gluey pitch seems to have been derived (distilled?) from birch bark. Some scientists demonstrated the process by burning a roll of birch bark in a pit, but they obviously did not use enough bark, and only got a smudge of goo. It’s a bit frustrating watching someone do something obviously wrong–since you’re filming this for TV, why not use a great big bunch of birch bark so you can get enough pitch to actually show us?

Anyway, looks like Neanderthals distilled this gluey stuff and then used it to help secure the flint tips to their spears, before thrusting them into the sides of enormous shaggy elephants, which are quite formidable animals. So the pitch (and bindings) had to be pretty darn good.

Neanderthals also seem to have buried their dead, though the show notes that their potential grave-goods pale in comparison to similar human burials.

The parts about Neanderthal DNA will be of interest to you if you don’t know about the Neanderthal/human DNA admixture business already, or you’ve heard about it but are still a little unclear on the details. The scientists interviewed claimed that it looks like there were a lot of interbreeding incidents rather than just a few, but “a lot” in this case does not necessarily mean “thousands”.

 

Cons: For a program that goes into depth on how inaccurate depictions of Neanderthals happened (ages ago, someone found a skeleton with arthritis and concluded that all Neanderthals were stooped,) their depiction of the homo Sapiens who first encountered the Neanderthals was also inaccurate.

The first encounters between humans and Neanderthals probably happened in the Middle East, shortly after h Sapiens left Africa, but before they had split into Asian and European branches. In other words, not to put too fine a point on it, whites did not yet exist. We’re not sure exactly when white skin evolved, but it probably wasn’t before h Sapiens got to Europe.

(Of course, it could be the other way around, and it’s the Bushmen who’ve changed since they split off.)

Either way, it’s pretty easy to assume things that are probably wrong, and the h Sapiens who first encountered h Neanderthals were probably more similar in appearance to modern Africans or Middle Easterners than Europeans.

A second issue occurred during a dramatization of the Neanderthal and h Sapiens DNA. Neanderthal DNA was depicted as red, and h Sapiens as blue. (Erm, I think. Unless I’ve got it backwards.) They then showed a “combined” DNA strand with blue and red pieces.

While this is a fine way to visualize what’s going on, I would just like to clarify that DNA isn’t actually blue or red, nor are there folks running around with mosaic red/blue variants.

You may be laughing (I burst out laughing at the sight of it,) but I know people who would very sincerely and devoutly insist that “Humans have different colored DNA from Neanderthals. I saw this program on PBS all about it, and I know PBS is accurate. You should watch the program!”

You can imagine how talking to these people makes me feel.

Finally, my last complaint is that there was no discussion of Neanderthal DNA in Native Americans!

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)

Right, so what’s up with Native Americans? You may have noticed that during the discussion with the map, no jellybeans were placed on the Americas at all. What a pity, when there’s still so much about the peopling of the Americas that we don’t know.

In the future, I’m hoping for similar documentaries about the Denisovans and their DNA admixture in modern humans.

Neanderthals!

So I still haven’t tracked down anything I consider a good source on the percent of Neanderthal DNA in people from particular regions of Europe, and I should note that at this point, I consider pretty much *everything* in the field of Neanderthal DNA in modern homo Sapiens quite speculative and not nearly has solid as people make it ought to be. But it’s still really interesting stuff, so here goes. I’ll start with a little background information in case you haven’t been following along:

1. Modern people tend to have a little bit of archaic DNA from non-human hominins. Pretty much everyone outside of Africa (including African Americans and even some Africans) has Neanderthal DNA; folks down in Papua New Guinea also have Denisovan DNA (I can’t remember if people outside of PNG have Denisovan.) People in Africa, I hear, have their own admixture from whoever else was living down in Africa. Oh, and people in Tibet have admixture from the hominins who used to live in Tibet before them.

2. Interestingly, the Neanderthal DNA does not appear to be concentrated where you’d think it would be. Sure, Neanderthals themselves hung out primarily in Europe and the Middle East, but American Indians seem to have the most Neanderthal DNA, followed by East Asians. (I consider these findings especially speculative.)

I have noticed in studying maps of different waves of human migrations that where one wave follows another, the first wave ends up way out in the fringes. Take, for example, the parts of Europe where people speak Celtic languages. Celtic languages were once widespread in Europe, covering France, Spain, Britain, Ireland, Switzerland, and a few other places, like possibly a town in Turkey. Today, Celtic languages are spoken in isolated pockets on the outer costs of Ireland, Scotland, and Wales. There are a few other isolated spots on the mainland coast where the languages persisted until fairly recently. Germanic peoples invaded all of these countries, taking them over and imposing their languages, until the Celtic languages are only left at the fringes, in places protected by their isolation.

So, likewise, perhaps Europe itself, being closer to Africa, had more invasions and so ended up with less Neanderthal DNA than the Americas, which were really bloody hard to invade.

There are a lot of other ways one group could get more Neanderthal DNA than another.

3. So how Neanderthal are you? On average, I believe non-African people have about 2.5% Neanderthal DNA.

For perspective, you have 32 great-great-great grandparents, who were probably born around 150 years ago, and 64 great-great-great-great grandparents, whom we’ll just neatly say were born around 170 years ago.

1/32 = 3.1%, so you’d expect to receive about 3.1% of your DNA from each of your 3xGreat Grandparents. 1/64 = 1.6%, so you get about 1.6% from each of your 4X Great Grandparents. So that’s where the average person’s Neanderthal contribution is–it’s like having one Neanderthal ancestor from the mid 1800s.

A lot of people claim to be ethnically Irish based on less.

4. I suspect Europe’s Neanderthal hotspot is Sardinia.

Speculations later.