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.

The Genghis Khans of Europe

They say that about 1 in 200 people alive today is descended from Genghis Khan (or one of his brothers, if he had any.) Obviously most of the Great Khan’s descendants are in Asia; what about the rest of the world?

from A Handful of Bronze Age Men Could have fathered two-thirds of Europeans
from A Handful of Bronze Age Men Could have fathered two-thirds of Europeans

From the article:

“Tracking [Y chromosome] mutations allows scientists to create a family tree of fathers and sons going back through time. … Two-thirds of modern European men are found on just three branches (called I1, R1a and R1b). Our results show that these branches each trace their paternal ancestry to a surprisingly recent individual (shown as red dots in Figure 1). By counting the number of mutations that have accumulated within each branch over the generations, we estimate that these three men lived at different times between 3,500 and 7,300 years ago.”

Female genetics–mitochondrial DNA–show no such feature. “… when looking at this maternal tree, there is no similar explosion. This indicates that whatever factors were responsible for this pattern were specific to men.”

This seems reasonably strong evidence that we aren’t just looking at something that could be explained away as founder/bottleneck effect, because I would expect such an effect to act equally on males and females. However, I don’t know if anyone has adequately addressed the question of patrilocality.

On a potentially related note, another study came up with this graph of Y chromosome diversity over time

From,  A recent bottleneck of Y chromosome diversity coincides with a global change in culture
From,
A recent bottleneck of Y chromosome diversity coincides with a global change in culture

 

Now if you ask me, these look like they’re describing the same phenomenon, but the dates are supposedly different.

A couple of thoughts:

1. I really really wish they’d made the Y Chromosome graph bigger and spread it out more so I can actually see what’s going on. According to the article summarizing the paper, the Siberian population did not suffer a decrease in Y chromosome diversity at this time, but I can’t tell it from looking at the graph.

2. Wow, look at the African Y chromosome diversity drop and then never fully recover. The Near East Y-diversity (the orange part) shoots up much higher than it was initially after the drop, as does the European. If the suspicion that farming was the cause of the drop is correct, then it looks like African Y chromosomes never quite recovered–consistent with the theory that African horticulture has traditionally been easy enough for women to do, leading to polygyny, leading to a few males dominating most of the women and the other males being excluded, etc. See, eg, West African Marriage and Child-Rearing Norms vs. African American Norms. (I’ve got another post on the subject, but it’s not going up for a few more weeks.)

3. What’s been happening to mtDNA diversity in the past few thousand years?

 

So was it agriculture? Or were did agriculture just make people sitting ducks for horse-born invaders? Or perhaps both?

Oops, Looks like it was People, not Pots

There’s an exciting new study on Bronze Age genetics that you’ve probably already heard about but I’m gonna post about anyway because stuff like this is kind of like our core competency around here.

Summary: Scientist people sequenced genomes (did fancy lab things with genetics) on 101 dead Europeans/Asians from a few thousand years ago, to try to figure out who they were and where they came from.

One of the big anthro/archeology debates over the past 70 years or so has been whether the different layers of cultural artifacts (eg, pots) represent things being traded while people stay put, or people invading and bringing their new stuff with them.

To put it in a modern context, if you saw a picture of people from Papua New Guinea taken in 1900, wearing traditional tribal clothes, and then saw a picture taken a few decades later of people from Papua New Guinea wearing Levi’s and T-shirts, you might wonder if the people of PNG had gotten some new clothes, or if some people wearing Levi’s had gone to PNG.

The archaeological assumption pre-1940 or so was generally that different layers of cultural artifacts represented actually different groups of people, who had probably invaded and slaughtered the previous group of people. For a variety of reasons that you can probably figure out on your own, this view fell into disrepute around the mid 1940s, and so was replaced with the peaceful assumption that new cultural artifacts probably spread primarily through trade, not warfare. This is expressed through the phrase, “Pots, not people,” meaning that the pots were moving around, not the people.

So now we can sequence ancient genomes and shit, so we can actually take a look at the people in ancient burials and try to figure out if people in Layer of Pots A are related to people in Layer of Pots B, or if they are a totally different group of people. This is like squinting at the photographs of Papua New Guineans and trying to figure out if the people wearing the clothes look like they come from the same group, but with lab tools and science.

From an archaeology/anthropology perspective, this is big stuff people have been debating about for over a century.

Conclusions: The Yamnaya are the Indo-Europeans (or proto-Indo-Europeans.) They started out around the Ukraine, then about 4,000 years ago, they spread out (cause they had horses and wagons and chariots and such with wheels,) toward the west and east. In Europe they became the Corded Ware Culture. The Corded Ware may have headed toward the Urals and became some of the ancestors of the Indo-Iranians, but that’s still fuzzy.

The Yamnaya had high (relatively) rates of lactose tolerance, so they probably helped spread that gene/the gene helped spread them. Blond hair and blue eyes are not Yamnaya traits–those came from elsewhere. They probably had pale skins, but so did most of the people already in Europe, so they didn’t change that.

I had already figured the Yamnaya were the PIEs (along with a bunch of other people paying even vague attention to the field,) but apparently my rough mental estimate of the time frame was off. 4,000 years ago is not that long–we have quite abundant records of life 2,000 years ago, so imagine what sorts of records or rumors those Greeks and Romans had about life 2,000 years before themselves.

There is much that we once naively took as fact, then skeptically decided was myth, then decided was fact again, like the existence of Troy. (Of course, there is also much that has turned out to be actually false. Like Herodotus’s dog-sized ants.) Perhaps some more of what seems mere myth in the Greek and Roman accounts will turn out to have some basis in history.

On the eastern end of the geographic range they surveyed, the steppe-folks out there were later replaced with a more Asian population that looks more closely related to the Native Americans (possibly descended from a population ancestral to both them and the Native Americans.)

I don’t know yet just how violent the invasion was–the existing European population was not wiped out, a la the Dorset. The groups mixed; modern Europeans (and many Asians) are a mixture of many population waves. But we do know now that these were people, not just their pots.