Race: The Social Construction of a Biological Reality, pt 2

Note: This post still contains a lot of oversimplification for the sake of explaining a few things.

Welcome back to our discussion of the geographic dispersion of humanity. On Tuesday, we discussed how two great barriers–the Sahara desert and the Himalayas + central Asian desert–have impeded human travelers over the millennia, resulting in three large, fairly well-defined groups of humans, the major races: Sub-Saharan Africans (SSA), Caucasians, and east Asians.

Of course, any astute motorist, having come to a halt at the Asian end of our highway, might observe that there is, in fact, a great deal of land in the world that we have not yet explored. So we head to the local shop and pick up a better map:

race2

Our new map shows us navigational directions for getting to Melanesia and Australia–in ice age times, it instructs us, we can drive most of the way. If there isn’t an ice age, we’ll have to take a boat.

900px-oceania_un_geoscheme_-_map_of_melanesia-svgThe people of Melanesia and Australia are related, the descendants of one of the first groups of humans to split off from the greater tribe that left Africa some 70k ago.

As the name “Melanesian” implies, they are quite dark-skinned–a result of never having ventured far from the equatorial zone.

Today, they live in eastern Indonesia, Papua New Guinea, Australia, and a smattering of smaller islands. (Notably, the Maori of New Zealand are Polynesians like the Hawaiians, not Melanesians, descendants of a different migration wave that originated in Taiwan.)

Fijian mountain warrior
Fijian mountain warrior with curly, “African” style hair

There is some speculation that they might have once been wider-spread than they currently are, or that various south-Asian tribes might be related to them, (eg, “A 2009 genetic study in India found similarities among Indian archaic populations and Aboriginal people, indicating a Southern migration route, with expanding populations from Southeast Asia migrating to Indonesia and Australia,”) but I don’t think any mainland group would today be classed as majority Melanesian by DNA.

They may also be related to the scattered tribes of similarly dark-skinned, diminutive people known as the Negritos:

Males from the Aeta people (or Agta) people of The Philippines, are of great interest to genetic, anthropological and historical researchers, as at least 83% of them belong to haplogroup K2b, in the form of its rare primary clades K2b1* and P* (a.k.a. K2b2* or P-P295*).[7] Most Aeta males (60%) carry K-P397 (K2b1), which is otherwise uncommon in the Philippines and is strongly associated with the indigenous peoples of Melanesia and Micronesia. Basal P* is rare outside the Aeta and some other groups within Maritime South East Asia. …

Naural blond hair
Two Melanesian girls from Vanatu (blond hair is common in Melanesian children.)

A 2010 study by the Anthropological Survey of India and the Texas-based Southwest Foundation for Biomedical Research identified seven genomes from 26 isolated “relic tribes” from the Indian mainland, such as the Baiga, which share “two synonymous polymorphisms with the M42 haplogroup, which is specific to Australian Aborigines“. These were specific mtDNA mutations that are shared exclusively by Australian aborigines and these Indian tribes, and no other known human groupings.[12]

A study of blood groups and proteins in the 1950s suggested that the Andamanese were more closely related to Oceanic peoples than African Pygmies. Genetic studies on Philippine Negritos, based on polymorphic blood enzymes and antigens, showed they were similar to surrounding Asian populations.[13]

Negrito peoples may descend from Australoid Melanesian settlers of Southeast Asia. Despite being isolated, the different peoples do share genetic similarities with their neighboring populations.[13][14] They also show relevant phenotypic (anatomic) variations which require explanation.[14]

In contrast, a recent genetic study found that unlike other early groups in Malesia, Andamanese Negritos lack the Denisovan hominin admixture in their DNA. Denisovan ancestry is found among indigenous Melanesian and Australian populations between 4–6%.[15][16]

Australian Aboriginal man
Australian Aboriginal man

However, the Negritos are a very small set of tribes, and I am not confident that they are even significantly related to each other, rather than just some short folks living on a few scattered islands. We must leave them for another day.

The vast majority of Aborigines and Melanesians live in Australia, Papua New Guinea, and nearby islands. They resemble Africans, because they split off from the rest of the out-of-Africa crew long before the traits we now associate with “whites” and “Asians” evolved, and have since stayed near the equator, but they are most closely related to–sharing DNA with–south Asians (and Indians.)

So we have, here, on the genetic level, a funny situation. Melanesians are–relatively speaking–a small group. According to Wikipedia, thee are about 12 million Melanesians and 606,000 Aborigines. By contrast, Tokyo prefecture has 13 million people and the total Tokyo metro area has nearly 38 million. Meanwhile, the Han Chinese–not a race but a single, fairly homogenous ethnic group–number around 1.3 billion.

Of all the world’s peoples, Melanesians/Aborigines are most closely related to other Asians–but this is a distant relationship, and those same Asians are more closely related to Caucasians than to Aborigines.

As I mentioned on Tuesday, the diagram, because it is 1-dimensional, can only show the distance between two groups at a time, not all groups. The genetic distance between Caucasians and Aborigines is about 60 or 50k, while the distance between Asians and Caucasians is around 40k, but the distance between Sub-Saharan Africans and ALL non-SSAs is about 70k, whether they’re in Australia, Patagonia, or France. Our map is not designed to show this distance, only the distances between individual pairs.

Some anthropologists refer to Bushmen as "gracile," which means they are a little shorter than average Europeans and not stockily built
Some anthropologists refer to Bushmen as “gracile,” which means they are a little shorter than average Europeans and not stockily built

Now if we hopped back in our car and zoomed back to the beginning of our trip, pausing to refuel in Lagos, we’d note another small group that has been added to the other end of the map: the Bushmen, aka the Khoi-San people. Wikipedia estimates 90,000 San and doesn’t give an estimate for the Khoi people, but their largest group, the Nama, has about 200,000 people. We’ll estimate the total, therefore, around 500,000 people, just to be safe.

The Bushmen are famous for being among the world’s last hunter-gatherers; their cousins the Khoi people are pastoralists. There were undoubtedly more of them in the past, before both Europeans and Bantus arrived in southern Africa. Some people think Bushmen look a little Asian, due to their lighter complexions than their more equatorial African cousins.

Genetically:

Various Y chromosome studies show that the San carry some of the most divergent (oldest) human Y-chromosome haplogroups. These haplogroups are specific sub-groups of haplogroups A and B, the two earliest branches on the human Y-chromosome tree.[48][49][50]

Mitochondrial DNA studies also provide evidence that the San carry high frequencies of the earliest haplogroup branches in the human mitochondrial DNA tree. This DNA is inherited only from one’s mother. The most divergent (oldest) mitochondrial haplogroup, L0d, has been identified at its highest frequencies in the southern African San groups.[48][51][52][53]

I loved that movie
The late Nǃxau ǂToma, (aka Gcao Tekene Coma,) Bushman star of “The Gods Must be Crazy,” roughly 1944-2003

In a study published in March 2011, Brenna Henn and colleagues found that the ǂKhomani San, as well as the Sandawe and Hadza peoples of Tanzania, were the most genetically diverse of any living humans studied. This high degree of genetic diversity hints at the origin of anatomically modern humans.[54][55]

Recent analysis suggests that the San may have been isolated from other original ancestral groups for as much as 100,000 years and later rejoined, re-integrating the human gene pool.[56]

A DNA study of fully sequenced genomes, published in September 2016, showed that the ancestors of today’s San hunter-gatherers began to diverge from other human populations in Africa about 200,000 years ago and were fully isolated by 100,000 years ago … [57]

So the total distance between Nigerians and Australian Aborogines is 70k years; the distance between Nigerians and Bushmen is at least 100k years.

When we zoom in on the big three–Sub-Saharan Africans, Caucasians, and Asians–they clade quite easily and obviously into three races. But when we add Aborigines and Bushmen, things complicate. Should we have a “race” smaller than the average American city? Or should we just lump them in with their nearest neighbors–Bushmen with Bantus and Aborigines with Asians?

I am fine with doing both, actually–but wait, I’m not done complicating matters! Tune in on Monday for more.

Ethnic Groups of India, Pakistan, Asia, and Australia

india

Source: Haak et al., Massive Migration from the steppe was a source for Indo-European langauges in Europe.

Note: There is a territorial dispute between India and Pakistan. I am not trying to wade into that dispute or pass judgment on who really controls what. Also, I don’t know what distinguishes the 4 Gujarati samples, so they’re just in ABC order.

And finally, greater Asia (plus Australia):

asia

Note that I had to leave off some groups from this map that appeared on earlier maps, like most of the Caucasian ethnicities. (Note that central Siberia is not actually as badly sampled as it looks, because this is a Mercator projection which makes Siberia look bigger than it actually is. Yes, I know, I don’t like Mercator projections, either, but it’s hard to find a nice, blank map with Asia on the left and Alaska on the right, and a cylindrical projection allows me to just switch the two halves without messing up the angles of the continents.)

And we’re done!

So who is White?

“White” is a nebulous category. “Black” is actually easier to define, because there’s a pretty hard boundary (the Sahara) between black Africa and everywhere else. To be fair, there are also groups like the Bushmen (who are more tawny brownish,) and the Pygmies who are genetically separate from other sub-Saharan Africans by over 100,000 years, but these are pretty small on the global scale. But “whites” and “Asians” occupy the same continent, and thus shade into each other.

If we use a strictly skin tone definition (as the world “white” implies) we can just pull up a map of global skin tone variation:

source: Wikipedia
source: Wikipedia

Of course, this implies that either Spaniards and Finns aren’t white, or Chinese and Eskimos are. Either way is fine, of course, though this would contradict most people’s usage. (And I kind of question that data on the Finns:

credit: The Postnational Monitor
credit: The Postnational Monitor)

These composites of faces from around the world offer us some more data, though depending on how they were made, they may not accurately reflect skin tone in all countries (ie, if the creator relied on pictures of famous people available on the internet, then these will reflect local beauty norms than group averages.)

(Plus, I wonder why the Romanians are pink.)

J. B. Huang has taken some of the Eurasian faces from this set and gone through the effort of trying to quantitize their shapes, as displayed in this graph (at least, that’s what I think they’re doing):

all_embeddingInterestingly, while some of the faces cluster together the way you might expect–China, Taiwan, Korea, and Japan are all near each other, as are Belgium and the Netherlands–many of the groupings are near random, eg, Mongolia, Turkey, and the Philippines. Hungary and Austria are closer to India and Japan than to Poland or Finland. The European faces are all over the map.

Maybe this doesn’t mean anything at all, or maybe it means that there’s a lot of variation in European faces.

This is actually not too surprising, given that modern Europeans are genetically descended from three different groups who conquered the peninsula in successive waves, leaving more or less of their DNA in different areas: the hunter gatherers who were there first, followed by farmers who spread out from Anatolia (modern Turkey,) followed by the “Indo-Europeans” aka the Yamnaya, who were part hunter gatherer (by DNA, not profession) and part another group whose origins have yet to be located, but which I call the “teal people” because their DNA is teal on Haak’s graph.

Oh yes, we are getting to Haak.

Click for full size
From Haak et al.

This isn’t the full graph, but it’s probably enough for our purposes. The European countries show a characteristic profile of Orange, Dark Blue, and Teal. (By contrast, the east Asian countries, which cluster closely together on the facial map, are mostly yellow with only a bit of red.)

Obviously DNA isn’t actually colored. It’s just a visual aid.

Haak’s graph makes it fairly easy to rule out the groups that are definitely different (at least genetically.) The American Indians, Inuit, West Africans, Chinese, and Aborigines are distinctly out. This leaves us with Europe, the Middle East, North Africa, India, and parts of central Asia/Siberia:

Europe

The Orange-centric region, which Haak et al arranged to display the movements of the Anatolian farmer people.

india

The heavily teal Indian section (The middle part, from Hazara-Tlingit, are obviously not Indian).

siberiaAnd finally some Siberian DNA.

Now, I could stare at these all day; I love them. They tell so many fascinating stories about people and where they went. Of the three ancestries found in Europeans, the oldest, the dark blue (hunter-gatherers,) is found throughout India, Siberia, and even the Aleutian islands (though I caution that some of this could just be because of Russians raping the Aleuts back in the day.) The dark blue appears to hit a particular low point in the Caucuses region, which of course is about where the teal got its start.

The orange–Anatolian farmers–shows up throughout the Middle East and Europe, but is near totally absent in India and Siberia. (Not much farming in Siberia!)

At a lower resolution (not pictured,) India, central Asia, and Siberia appear to have a mix of–broadly speaking–“European” and “Asian” ancestry. (Not too surprising, since they are in the middle of the continent.) Obviously the middle of Asia is a big crossroads between different groups–red (Siberian) yellow (east Asian) teal and dark blue, and bits of the same DNA that shows up in the Eskimo (Inuit) and Aleuts.

But this is all kind of complicated. Luckily for us, this is only one way to visualize DNA–I’ve got others!

Credit Robert Lindsay, Beyond Highbrow
Credit Robert Lindsay, Beyond Highbrow

If you’re not familiar with these sorts of trees, the basic story is that geneticists gathered DNA samples (from spit, I think, which is pretty awesome,) from ethnic groups from all over the world, and then measured how many genes they have in common. More genes in common = groups more closely related to each other. Fewer genes = more genetic distance from each other.

Since different genetic samples and computer models are different, different teams have produced slightly different genetic trees.

Note that since the tree is constructed by comparing # of genes two groups have in common, a group could end up in a particular spot because it is descended from a common ancestor with other nearby groups, or because of mixing between two groups. Ashkenazi Jews, for example, cluster with southern Europeans because they’re about half Italian (and obviously half ancient Israeli.) Here’s another chart, giving us another perspective:

I totally stole this from Razib Khan, didn't I?
I totally stole this from Razib Khan–though he got it from here.

This chart also shows us genetic differences between groups, with strong clustering among African and East Asians, respectively, and then a sort of scattered group of Europeans and Indians (South Asians.)

Also credit Robert Lindsay
Also credit Robert Lindsay

Neither of these graphs shows Siberians or central Asians in great detail, because they are tiny groups, but I think it’s safe to say the Siberians at least cluster near their neighbors, the other Asians and far-north Americans.

The central and south Asians, though, are quite the interesting case!

Between archaeology and genetics, we’ve been able to trace the path of human expansion, from central Africa to the world:

I think this map came from that recent article about possibly finding traces of the first out-of-Africa event in Papuans.
I think this map came from that recent article I discussed in the post about possibly finding traces of the first out-of-Africa event in Papuans.

Since this post is already image heavy, here is a graph showing finer detail on European and North African groups, Moroccans, (Berbers), Aleut woman, Sardinians, Sami (Lapps), Iranians, Gujarati, (another), Dravidian, Brahmin, Dalits, Altai, Uyghur, Selkup. (Look at the pictures!)

Well, ultimately, there’s no hard division between most ethnic groups or races–you can draw dividing lines where you want them. The term “white” implies dermal paleness, of course, so you may prefer a narrower definition for “white” than “Caucasian.” Greater minds than mine have already covered the subject in more authoritative detail, of course. I merely offer my thoughts for entertainment.

Why Geneticists get touchy about Epigenetics

Disclaimer: I am not a geneticist. For those of you who are new here, this is basically a genetics fan blog. I am trying to learn about genetics, and you know what?

Genetics is complicated.

I fully admit that here’s a lot of stuff that I don’t know yet, nor fully understand.

Luckily for me, there are a few genetics basics that are easy enough to understand that even a middle school student can master them:

  1. “Evolution” is the theory that species change over time due to some individuals within them being better at getting food, reproducing, etc., than other individuals, and thereby passing on their superior traits to their children.
  2. “Genes,” (or “DNA,”) are the biological code for all life, and the physical mechanism by which traits are passed down from parent to child.
  3. “Mendel squares” work for modeling the inheritance of simple traits
  4. More complicated trait are modeled with more complicated math
  5. Lamarckism doesn’t work.

Lamarck was a naturalist who, in the days before genes were discovered, theorized that creatures could pass on “acquired” characteristics. For example, an animal with a relatively normal neck in an area with tall trees might stretch its neck in order to reach the tastiest leaves, and then pass on this longer-neck to its children, who would also stretch their necks and then pass on the trait to their children, until you get giraffes.

A fellow with similar ideas, Lysenko, was a Soviet Scientist who thought he could make strains of cold-tolerant wheat simply by exposing wheat kernels to the cold.

We have the luxury of thinking that Lysenko’s ideas sound silly. The Soviet peasants had to actually try to grow his wheat, and scientists who pointed out that this was nonsense got sent to the gulag.

The problem with Lamarckism is that it doesn’t work. You can’t make wheat grow in Antarctica by sticking it in your freezer for a few months and animals don’t have taller babies just because you stretch their necks.

So what does this have to do with epigenetics?

Pop science articles talk about epigenetics as if it were Lamarckism. Through the magic of epigenetic markers, acquired traits can supposedly be passed down to one’s children and grandchildren, infinitely.

Actual epigenetics, as scientists actually study it, is a real and interesting field. But the effects of epigenetic changes are not so large and permanent as to substantially change most of the way we model genetic inheritance.

Why?

Epigenetics is, in essence, part of how you learn. Suppose you play a disturbing noise every time a mouse smells cherries. Pretty soon, the mouse would learn to associate “fear” and “cherry smell,” and according to Wikipedia, this gets encoded at the epigenetic level. Great, the mouse has learned to be afraid of cherries.

If these epigenetic traits get passed on to the mouse’s children–I am not convinced this is possible but let’s assume it is–then those children can inherit their mother’s fear of cherries.

This is pretty neat, but people take it too far when they assume that as a result, the mouse’s fear will persist over many generations, and that you have essentially just bred a new, cherry-fearing strain of mice.

You, see, you learn new things all the time. So do mice. Your epigenetics therefore keep changing throughout your life. The older you are, the more your epigenetics have changed since you were born. This is why even identical twins differ in small ways from each other. Sooner or later, the young mice will figure out that there isn’t actually any reason to be afraid of cherries, and they’ll stop being afraid.

If people were actually the multi-generational heirs of their ancestors’ trauma, pretty much everyone in the world would be affected, because we all have at least one ancestor who endured some kind of horrors in their life. The entire continent of Europe should be a PTSD basket case due to WWI, WWII, and the Depression.

Thankfully, this is not what we see.

Epigenetics has some real and very interesting effects, but it’s not Lamarckism 2.0.

Updated Tentative map of Neanderthal DNA

Picture 1

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.

Native Americans and Neanderthal DNA

Since “Do Native Americans have Neanderthal DNA?” (or something similar) is the most popular search that leads people to my blog, I have begun to suspect that a clarification is in order.

Native Americans (Indians) are not Neanderthals. They are not half or quarter or otherwise significantly Neanderthal. If they were, they would have very noticeable fertility problems in mixed-race relationships.

They may have slightly higher than average Neanderthal admixture than other groups, but that is extremely speculative I don’t know of any scientists who have said so. We’re talking here about quite small amounts, like 0.5%, most of which appears to code for things like immune response and possibly some adaptations for handling long, cold winters. None of this appears to code for physical traits like skull shape, which have been under different selective pressures over the past 40,000 years.

As much as I would love to discover a group with significant Neanderthal DNA, that’s just not something we’ve found in anyone alive today.

Sorry, guys.

Haak et al’s full graph

WARNING: This post is full of speculations that I am recording for my own sake but are highly likely to be wrong!

Click for full size
From Haak et al.

Hey, did you know that this isn’t actually Haak et al’s full DNA graph? The actual full dataset looks like this:

 

Picture 1Picture 2

 

 

 

 

 

 

Isn’t it beautiful?

You’re going to have to click for the full size–sorry I couldn’t fit it all into one screen cap. I’m also sorry that the resolution is poor, and therefore you can’t read the labels (though you should be able to figure out which is which if you just compare with the smaller graphic at the top of the screen. (Supposedly there’s a higher resolution version of this out there, but I couldn’t find it.)

Why the reliance on a greatly cropped image? Just the obvious: the big one is unwieldy, and most of the data people are interested in is at the top.

But the data at the bottom is interesting, too.

On the lefthand side of the graph, we have a measure of granularity–how much fine detail we are getting with our genetic data. The bottom row, therefore, shows us the largest genetic splits between groups–presumably, the oldest splits.

From left to right, we have selections of different ethnic groups’ DNA. Old European skeletons constitute the first group; the mostly pink with some brown section is Native North/South American; the blue and green section is African; the big wide orange section is mostly European and Middle Eastern; then we have some kind of random groups like the Inuit (gold), Onge (pink, Indian Ocean), and Australian Aborigines; the heavily green areas are India; the mixed-up area splitting the green is Eurasian steppe; the yellow area is East Asian; and the final section is Siberian.

Level One: Sub-Saharan Africa (SSA) vs. Non-Sub-Saharan Africa

The bottom row shows us, presumably, the oldest split, between the orange and the blue. All of these light blue groups, from the Ju Hoan (Bushmen/San) to the Yoruba (Nigeria,) Somalis to Hadza (Tanzania,) African Americans to Shua (Khoe speakers of Namibia/Botswana,) are from Africa–sub-Saharan Africa, I’d wager (though I’m not sure whether Ethiopia and Somalia are considered “sub-Saharan.”)

All of the other groups–including the sampled north-African groups like Saharawari (from Western Sahara,) Tunisians, Algerians, Mozabites (Algeria,) and Egyptians–show up in orange.

(Note: Light green and orange are completely arbitrary color choices used to represent the DNA in these graphs; there is nothing inherently “orange” or “green” or any other color about DNA.)

I would not actually have predicted this–other studies I have read predicted that the split between the Bushmen, Pygmies, and other groups in Africa went back further in Africa than the split between Africans and non-Africans, but perhaps the Sahara has been the most significant barrier in human history.

Interestingly, the split is not absolute–there are Sub-Saharan groups with non-SSA admixture, and non-SSA groups with SSA admixture. In fact, most of the SSA groups sampled appear to have some non-SSA admixture, which probably has something to do with back-migration over the centuries; predictably, this is highest in places like Somalia and Ethiopia, fairly high along the east coast of Africa (which has historically been linked via monsoon trade routes to other, non-African countries;) and in African Americans (whose admixture is much more recent.) (Likewise, the admixture found in some of the hunter-gatherer peoples of southern Africa could be relatively recent.)

The Non-SSA groups with the most SSA admixture, are north African groups like the aforementioned Algerians and Tunisians; Middle Eastern groups like the Druze, Syrians, Bedouins, Jordanians, etc.; “Mediterranean” groups like the Sicilians and Maltese; various Jewish groups that live in these areas; and a tiny bit that shows up in the people of the Andaman Islands, Australia, and PNG.

(Oh, and in various old European skeletons.)

Level Two: “Western” vs. “Eastern”

Moving on to level two, we have the next big split, between “Easterners” (mostly Asians) and “Westerners” (mostly Europeans and Middle-Easterners.)

Natives of North/South America, Inuits, Andaman Islanders, Australian Aborigines, Papuans, the Kharia (an Indian tribe that has historically spoken a non-Indo-European language,) some central or northern Asian steppe peoples like the Evens (Siberians,) and of course everyone from the Kusunda (Nepal) through China and Japan and up through, well, more Siberians like the Yakuts, all show up as mostly yellow.

Everyone from Europe, the Middle East, the Caucuses, and all of the sampled Indian populations except the Kharia have orange.

A bunch of little groups from the middle of Eurasia show up as about half-and-half.

Interestingly, some of the older European hunter-gatherer skeletons have small quantities of “Eastern” DNA; this may not represent admixture so much as common ancestry. It also shows up, predictably, in Turkey and the Caucuses; in Russia/Finns; tiny quantities in places like the Ukraine; and quite significantly in India.

Significant “Western” admixture shows up in various Natives North/South Americans (probably due to recent admixture,) the Andaman Islands, Aborigines, PNG, (this may represent something to do with a common ancestor rather than admixture, per se,) and Siberia.

Level Three: Native North/South Americans vs. “Easterners”

At this point, the “light pink” shows up in all of the sampled indigenous tribes of North and South America. A fair amount of it also shows up in the Inuit, and a small quantity in various Siberian tribes. A tiny quantity also show up in some of the older European skeletons (I suspect this is due to older skeletons being more similar to the common ancestors before the splits than trans-Atlantic contact in the stone age, but it could also be due to a small Siberian component having made its way into Europe.)

Even at this level, there is a big difference evident between the groups from Central and South America (almost pure pink) and those from northern North America, (significant chunk of orange.) Some (or all) of that may be due to recent admixture due to adoption of and intermarrying with whites, but some could also be due to the ancestors of the Chipewyans etc. having started out with more, due to sharing ancestors from a more recent migration across the Bering Strait. I’m speculating, of course.

Level Four: Intra-African splits

I don’t know my African ethnic groups like I ought to, but basically we have the Bushmen (aka San,) and I think some Khoe / Khoi peoples in green, with a fair amount of green also showing up in the Pygmies and other hunter-gatherers like the Hadza, plus little bits showing up in groups like the Sandawe and South African Bantus.

Level Five: Australian Aborigines, PNG, and Andamanese split off.

Some of this DNA is shared with folks in India; a tiny bit shows up in central Asia and even east Asia.

Level Six: Red shows up.

This reddish DNA is found in all “Siberian” peoples, people who might have moved recently through Siberia, and people who might be related to or had contact with them. It’s found throughout East Asia, eg, Japan and China, but only found in high quantities among the Inuit and various Siberian groups. At this resolution, oddly, no one–except almost the Itelmen and Koryak–is pure reddish, but at higher resolutions the Nganasan are, while the Itelmen and Koryak aren’t.

Level Seven: The “Indos” of the Indo-Europeans show up

Although no pure light green people have yet been found, their DNA shows up everywhere the Indo-Europeans (aka Yamnaya) went, with their highest concentration in India. Perhaps the light green people got their start in India, and later a group of them merged with the dark blue people to become the Yamnaya, a group of whom then migrated back into India, leaving India with a particularly high % of light green DNA even before the dark blue shows up.

Interestingly, some of this light green also show up in the Andamanese.

Level Eight: The “Europeans” of the Indo-Europeans show up

The dark blue color originates, in the left-hand side of the graph, with a several-thousand years old population of European hunter-gatherers which, as you can see in the slightly younger populations on the far left, nearly got wiped out by a nearly pure orange population of farmers that migrated into Europe from the Middle East. This dark blue population managed to survive out on the Eurasian Steppe, which wasn’t so suited to farming, where it merged with the light-green people. They became the Yamnaya aka the Indo-Europeans. They then spread back into Europe, the Middle East, India, central Asia, and Siberia. (The dark blue in modern Native American populations is probably due to recent admixture.)

Level Nine: The Hadza

The Hadza (a hunter-gatherer people of Tanzania) now show up as bright pink. No one else has a lot of bright pink, but the Pygmies (Mbutu and Biaka,) as well as a variety of other eastern-African groups located near them, like the Luo, Masai, and the Somalis have small amounts.

Level Ten: The Onge (Andamanese)

Not much happens here, but the Onge (from the Andaman Islands) turn peach and stay that way. It looks like a small amount of peach DNA may also be found across part of India (southern India, I’m assuming.)

Level Eleven: Chipewyans (North America)

The Chipewyans turn brown; brown is also found in small quantities in Central America, in moderate quantities in eastern North America, and in the Eskimo/Inuit.

Level Twelve: Pygmies

The Biaka and Mbuti Pygmies differentiate from their neighbors. Tiny quantities of Pygmy DNA found in probably-nearby peoples.

Level Thirteen: Inuit/Eskimo

They become distinctly differentiated from other North American or Siberian tribes (olive green.), Their olive green shade is found in small quantities in some Siberian tribes, but interestingly, appears to be totally absent from other Native American tribes.

Level Fourteen: Horn of Africa

A dusty peach tone is used for groups in the Horn of Africa like the Somalis and Ethiopians, as well as nearby groups like the Dinka. Small amounts of dusty peach are are also found along the East Africa, North Africa, and the Middle East. Smaller amounts appear to be in a variety of other groups related to the Bushmen.

Level Fifteen: The light green turns teal

All of the light green in Europe turns teal, but much of the light green in India stays light green. (Teal also shows up in India.) I have no idea why, other than my aforementioned theory that India had more light green to start with.

Level Sixteen: Amazon Rainforest tribes

The Kuritiana and Suri show up in light olive; light olive is also found in small quantities in other parts of Central and South America, and tiny bits in parts of North America, and maybe tiny amounts in the Eskimo but I don’t see any in the Chukchi, Itelmen, etc.

Level Seventeen: Bedouins

The Bedouins turn light purple; this DNA is also found through out the Middle East, Turkey, North Africa, the Mediterranean (eg Sicily), Greece, Albania, Spain, Bulgaria, Ashkenazim, and a tiny bit In India.

Level Eighteen: Some Bushmen appear to split off from some other Bushmen.

I don’t know much about these groups.

Level Nineteen: Nothing interesting appears to happen.

Please remember that all of this is me speculating. I am definitely not an educated source on these matters, but I hope you’ve had as much fun as I’ve had peering at the DNA and thinking about how people might have moved around and mixed and split to make the colors.

 

The Indigenous People of Europe

Do you know how long I've been waiting to use this?

The settlement in Cambridgeshire, which had been buried for 3,000 years, was discovered when the tops of crude protest signs were spotted above layers of mud.

Archaeologist Helen Archer said: “The signs, which include ‘Any old iron? NO THANKS,’ and ‘IRON? IR NO,’ a primitive attempt at wordplay, show that the residents were up in arms about climate-based migration patterns.

Note: The Daily Mash is a humor/satire site, similar to The Onion.

Anyway, on to the genetics!

From Haak et al, rearranged by me
From Haak et al, rearranged by me

Click for full size

Haak et al. made this graph, but I rearranged it so that the oldest samples are on the left and the newest ones are on the right. When multiple samples were about the same age, I ordered them from west to east (that is, from left to right as you look at a standard map. Unless you are in Australia.) I’ve added the dates (shown as ranges) that were in Haak’s paper. Note the asterisk under Karsdorf–those dates are still uncertain.

The first three genomes are from super old skeletons found out in, like, Russia. I don’t know why they look so crazy–maybe because the DNA is really old and so not very good, or maybe because they actually had a bunch of different DNA in them, or maybe because they’re ancestral to a bunch of different groups. I don’t know! Luckily, it doesn’t really matter for today’s post, so I’ll investigate them later.

Approximately 28,000 years later, we have the Blue People, also known as “Western European Hunter Gatherers,” or WHG. There were people in Europe in intervening 28,000 years; they just aren’t on the table, and I don’t know if anyone has successfully sequenced their genomes yet. (More research required.)

As you might guess, the WHG people hunted and gathered. They had stone tools, and were quite widespread, ranging from Spain (the La Brana1 site,) to Sweden to Samara, Russia (and probably beyond.)

And then some new guys showed up: Farmers.

Known as the Early Eurasian Farmers (EEF,) they first appear on our graph in Starcevo, Serbia, their DNA in orange. They came from the Middle East (the birthplace of agriculture,) bringing their wheat, permanent settlements, and livestock.

Why isn't it in English? Oh, well. We'll manage.
Neolithic cultures of Europe–Starcevo is i the lower right-hand corner.

These farmers quickly overran the hunter-gatherers throughout western Europe (though the northern extremes held out longer, most likely due to crops that originated in the Middle East taking a while to adapt to the harsh Scandinavian climate.)

300px-Neolithic_expansion.svg (source: Wikipedia)

The hunter gatherers disappeared (most likely slaughtered by the farmers, but perhaps merely overwhelmed numerically) but their DNA lives on in the descendants of those first farmers. Some groups may have combined willingly–others, as the spoils of war. Within the Farmers’ range, the only place the hunter-gatherers managed to live on appears to be a small island off the coast of Sweden (the second “Skoglund” sample.)

But to the east, out on the Eurasian steppes, the hunter-gatherers lived on. The steppes are known more for their rampaging hordes than their farmers, and this is exactly what they became.

The Yamnaya, as we now call them, are about half WHG and half some new population (I call them the Teal People.) As far as I know, no “pure” teal people have yet been found, but teal DNA is all over the place, from India to Spain.

Teal and blue DNA in India central Asia, and Siberia:

IndiaandSteppe

The Yamnaya are also known as the Proto-Indo-Europeans–the guys who spoke the language ancestral to all of today’s Indo-European languages. And like all conquering barbarian hordes, they expanded out of their homeland in present-day southern Russia (north of the Caucuses,) and conquered everything in their path.

Just eyeballing the graph, it looks like the resulting peoples are about half Yamnaya, and about half EEF. This tri-part inheritance is still seen in every European population (and some of their neighbors) today:

Europe

If we didn’t have the ancient DNA–or if we had less of it–it would be easy to think that the Blue component in modern Europeans had come directly from the ancient WHG population that lived in their particular area. Instead, much (if not most) of the modern “blue” component hails from the steppes of Russia–a remarkable comeback for the WHGs.

Oh, and the “indigenous” people of Europe? They’re all indigenous to the continent.

Some more helpful graphs, maps, and information:

From Haak et al.
From Haak et al.
From Haak et al.
From Haak et al.
From Haak et al.
From Haak et al.

On the Iceman, aka Otzi: found in the Alps on the Italian-Austrian border; Same age as Sweden, between 3359 and 3105 BCE. (Hailed from the vicinity of Feldthurns, Italy.)

Analysis of the mtDNA of Ötzi the Iceman, the frozen mummy from 3,300 BC found on the AustrianItalian border, has shown that Ötzi belongs to the K1 subclade. It cannot be categorized into any of the three modern branches of that subclade (K1a, K1b or K1c). The new subclade has provisionally been named K1ö for Ötzi.[14] Multiplex assay study was able to confirm that the Iceman’s mtDNA belongs to a new European mtDNA clade with a very limited distribution amongst modern data sets.[15]” (source)

Otzi ate grain but was lactose intolerant.

His Y DNA is haplogroup G, which is now rare in Europe:

Haplogrupo_G_(ADN-Y)

Various estimated dates and locations have been proposed for the origin of Haplogroup G. The National Geographic Society places haplogroup G origins in the Middle East 30,000 years ago and presumes that people carrying the haplogroup took part in the spread of the Neolithic.[2] Two scholarly papers have also suggested an origin in the Middle East, while differing on the date. …

Haplogroup G2a(SNP P15+) has been identified in neolithic human remains in Europe dating between 5000-3000BC. Furthermore, the majority of all the male skeletons from the European Neolithic period have so far yielded Y-DNA belonging to this haplogroup. The oldest skeletons confirmed by ancient DNA testing as carrying haplogroup G2a were five found in the Avellaner cave burial site for farmers in northeastern Spain and were dated by radiocarbon dating to about 7000 years ago.[5] At the Neolithic cemetery of Derenburg Meerenstieg II, north central Germany, with burial artifacts belonging to the Linear Pottery culture, known in German as Linearbandkeramik (LBK). This skeleton could not be dated by radiocarbon dating, but other skeletons there were dated to between 5,100 and 6,100 years old. The most detailed SNP mutation identified was S126 (L30), which defines G2a3.[6] G2a was found also in 20 out of 22 samples of ancient Y-DNA from Treilles, the type-site of a Late Neolithic group of farmers in the South of France, dated to about 5000 years ago.[7] The fourth site also from the same period is the Ötztal of the Italian Alps where the mummified remains of Ötzi the Iceman were discovered. Preliminary word is that the Iceman belongs to haplogroup G2a2b [8] (earlier called G2a4).

Haplogroup G2a2b is a rare group today in Europe. (source)

Back on the Otzi page:

By autosomal DNA he is most closely related to southern Europeans, especially to the geographically isolated populations of the two Mediterranean islands of Sardinia and Corsica.[41][42]

… In October 2013, it was reported that 19 modern Tyrolean men were related to Ötzi. Scientists from the Institute of Legal Medicine at Innsbruck Medical University had analysed the DNA of over 3,700 Tyrolean male blood donors and found 19 who shared a particular genetic mutation with the 5,300-year-old man, which led them to identify the link.[46]

Hungary Gamba CA= Copper age, 3,300 BC-2,700 AD

From an analysis of the Gamba site:

The Great Hungarian Plain was a crossroads of cultural transformations that have shaped European prehistory. Here we analyse a 5,000-year transect of human genomes, sampled from petrous bones giving consistently excellent endogenous DNA yields, from 13 Hungarian Neolithic, Copper, Bronze and Iron Age burials including two to high (~22 × ) and seven to ~1 × coverage, to investigate the impact of these on Europe’s genetic landscape. These data suggest genomic shifts with the advent of the Neolithic, Bronze and Iron Ages, with interleaved periods of genome stability. The earliest Neolithic context genome shows a European hunter-gatherer genetic signature and a restricted ancestral population size, suggesting direct contact between cultures after the arrival of the first farmers into Europe. The latest, Iron Age, sample reveals an eastern genomic influence concordant with introduced Steppe burial rites. We observe transition towards lighter pigmentation and surprisingly, no Neolithic presence of lactase persistence.

Stuttgart EN:

To investigate European population history around the time of the agricultural transition, we sequenced complete genomes from a ~7,500 year old early farmer from the Linearbandkeramik (LBK) culture from Stuttgart in Germany and an ~8,000 year old hunter-gatherer from the Loschbour rock shelter in Luxembourg. We also generated data from seven ~8,000 year old hunter-gatherers from Motala in Sweden. We compared these genomes and published ancient DNA to new data from 2,196 samples from 185 diverse populations to show that at least three ancestral groups contributed to present-day Europeans. The first are Ancient North Eurasians (ANE), who are more closely related to Upper Paleolithic Siberians than to any present-day population. The second are West European Hunter-Gatherers (WHG), related to the Loschbour individual, who contributed to all Europeans but not to Near Easterners. The third are Early European Farmers (EEF), related to the Stuttgart individual, who were mainly of Near Eastern origin but also harbored WHG-related ancestry. We model the deep relationships of these populations and show that about ~44% of the ancestry of EEF derived from a basal Eurasian lineage that split prior to the separation of other non-Africans.(bold mine.)

Ancient_North_Eurasian_admixture European_hunter-gatherer_admixture Neolithic_farmer_admixture

Source for the maps.

Iosif Lazaridis et al's model of modern European genetic origins.
Iosif Lazaridis et al’s model of modern European genetic origins.
Also from Iosif Lazaridis et al.'s paper, " Ancient human genomes suggest three ancestral populations for present-day Europeans"
Also from Iosif Lazaridis et al.’s paper, “Ancient human genomes suggest three ancestral populations for present-day Europeans” h/t Dienekes:

 Analysis of ancient DNA can reveal historical events that are difficult to discern through study of present-day individuals. To investigate European population history around the time of the agricultural transition, we sequenced complete genomes from a ~7,500 year old early farmer from the Linearbandkeramik (LBK) culture from Stuttgart in Germany and an ~8,000 year old hunter-gatherer from the Loschbour rock shelter in Luxembourg. We also generated data from seven ~8,000 year old hunter-gatherers from Motala in Sweden. We compared these genomes and published ancient DNA to new data from 2,196 samples from 185 diverse populations to show that at least three ancestral groups contributed to present-day Europeans. The first are Ancient North Eurasians (ANE), who are more closely related to Upper Paleolithic Siberians than to any present-day population. The second are West European Hunter-Gatherers (WHG), related to the Loschbour individual, who contributed to all Europeans but not to Near Easterners. The third are Early European Farmers (EEF), related to the Stuttgart individual, who were mainly of Near Eastern origin but also harbored WHG-related ancestry. We model the deep relationships of these populations and show that about ~44% of the ancestry of EEF derived from a basal Eurasian lineage that split prior to the separation of other non-Africans.

I'm sorry, I forgot where this came from
I’m sorry, I forgot where this came from.

See also:

Significant genetic differentiation between Poland and Germany follows present-day political borders, as revealed by Y-chromosome analysis, by Kayser M. et al:

To test for human population substructure and to investigate human population history we have analysed Y-chromosome diversity using seven microsatellites (Y-STRs) and ten binary markers (Y-SNPs) in samples from eight regionally distributed populations from Poland (n = 913) and 11 from Germany (n = 1,215). Based on data from both Y-chromosome marker systems, which we found to be highly correlated (r = 0.96), and using spatial analysis of the molecular variance (SAMOVA), we revealed statistically significant support for two groups of populations: (1) all Polish populations and (2) all German populations. … The same population differentiation was detected using Monmonier’s algorithm, with a resulting genetic border between Poland and Germany that closely resembles the course of the political border between both countries. The observed genetic differentiation was mainly, but not exclusively, due to the frequency distribution of two Y-SNP haplogroups and their associated Y-STR haplotypes: R1a1*, most frequent in Poland, and R1*(xR1a1), most frequent in Germany. We suggest here that the pronounced population differentiation between the two geographically neighbouring countries, Poland and Germany, is the consequence of very recent events in human population history, namely the forced human resettlement of many millions of Germans and Poles during and, especially, shortly after World War II.

And Iron Age and Anglo-Saxon genomes from East England reveal British migration history by Schiffels et al., h/t Steve Sailer

British population history has been shaped by a series of immigrations, including the early Anglo-Saxon migrations after 400 CE. … Here, we present whole-genome sequences from 10 individuals excavated close to Cambridge in the East of England, ranging from the late Iron Age to the middle Anglo-Saxon period. … we estimate that on average the contemporary East English population derives 38% of its ancestry from Anglo-Saxon migrations. … Using rarecoal we find that the Anglo-Saxon samples are closely related to modern Dutch and Danish populations, while the Iron Age samples share ancestors with multiple Northern European populations including Britain.

Tentative map of Neanderthal (and Denisovan) DNA in humans

I couldn’t find one, so I made one:
neandermap

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.