A Royal Elite in Neolithic Ireland?

The results have just been published of DNA studies on bones from Neolithic tombs in Ireland, dating to between 4,000 and 2,500 BC. The burial that is getting the most attention was buried in the heart of Newgrange, the largest Neolithic tomb in Britain, around 3.200 BC. Science News:

A man buried in a huge, roughly 5,200-year-old Irish stone tomb was the product of incest, a new study finds.

DNA extracted from the ancient man’s remains displays an unusually large number of identical versions of the same genes. That pattern indicates that his parents were either a brother and sister or a parent and child, a team led by geneticists Lara Cassidy and Daniel Bradley of Trinity College Dublin reports June 17 in Nature.

That new DNA discovery combined with the monumental tomb suggests that ruling families who wielded enough power to direct big building projects emerged among some early European farming communities, the researchers contend.

This is quite fascinating. It's hard for Americans to understand how large these Neolithic tombs and temples loom in the historical imaginations of many people in Ireland and Britain. There has been an industry of study and speculation about the tombs and the people who built them for 350 years. Every sort of theory has been proposed, from purely egalitarian societies to rule by priest kings to aliens.

A single case of an incestuously bred leader does not prove anything, but it does suggest a hereditary elite with religious associations. This could be our first bona fide Neolithic priest king.

Then again, it could just be a priest. In ancient Egypt and among the Inca it was the rulers who went in for incest, but among some Polynesian and African societies the practice was limited to priestly orders which did not have great political power. Other then the tombs themselves, there is not much sign of a ruling elite in Neolithic Ireland: no houses bigger than others, not much in the way of luxury goods. The tombs themselves were communal affairs within which many people were buried, or in some cases stashed until they had moldered to bones before being taken somewhere else.

But then again maybe the tombs were so important to these people that being buried in the core chamber was all the sign of status anyone needed.

Anyway this is fascinating, and another way that the study of ancient DNA has shed new light on questions that have been argued over for centuries.

The Beaker Folk and a Different Sort of Genetic History

Much of the history coming from paleogenetics has been rather grim, about how certain groups conquered others and almost completely replaced them. For example, the latest estimate is that 90 to 95% of the people of Britain were replaced after a Bronze Age invasion,  which may have been accompanied by bubonic plague.

But not everywhere. Data from Scandinavia suggests that many hunter-gatherers there survived and interbred with invading farmers, contributing up to a third of the genes of late Neolithic people. Since farmers generally live at higher populations densities, this implies a fairly equal contribution to future genes and a whole lot of intermixing. 

Distribution of the Bell Beaker Culture

And now there is some interesting data about the formation of the Bell Beaker people, who dominated parts of western Europe between 2700 and 2000 BC. Archaeologists long ago recognized that Beaker culture had two homelands, one in Portugal and one in the low countries around the mouth of the Rhine. Genetic studies showed that the two groups were not closely related. The southern group were mostly descended from neolithic farmers, while the northern group were like the Corded Ware people, who had a lot of genes from steppes invaders. Now new data shows that over time the Bell Beaker people interbred until most of them were a mix of Portuguese and Corded Ware types. Somehow these two groups, with different genetic histories and originating in different ecological zones, established a common culture with much interbreeding.

The current consensus is that many elements of Bell Beaker culture originated in Portugal. Somehow they spread that culture to northern peoples, who took it up with great enthusiasm, and then intermarried with southern folk, at least at the elite level.

So it wasn't all conquest and replacement.

Archaeology in the 2010s: the Paleogenetics Revolution

In the past decade, by far the most important development in archaeology has been the technology of paleogenetics, which is allowing us to answer questions I thought would be debated forever.

The technology works like this: DNA is chemically extracted from bone or other human remains and run through a sequencer. Powerful computers then read the various DNA sequences that emerge and discard all those not related to the problem at hand, such as viruses or bacteria, which are often the vast majority of the sample. The human DNA -- or sometimes other species, if that is what is being studied -- is then compared to databases of human genomes. It is rare for a nearly complete genome to be discovered; a genome is considered "high quality" if it is more than 5% complete. But a 5% sample of the 3 billion base pairs in the human genome is usually enough for high quality statistics. The differences between different human populations are small, on the order of 0.1%. Again, with 3 billion base pairs to work with the differences still stand out.

But I want to emphasize that all of this statistical, and it depends on assumptions made about which mutations represent important forking points in our genealogies and so on. I think this is great science but it is still very new and some of what I write below may turn out to be wrong. Most of it may turn out to be oversimplified.

I would summarize the main discoveries of paleogenetics so far as follows:

1) Humans interbred with other hominid species such as Neanderthals and Denisovans. Outside of Africa, humans are 1% to 1.5% Neanderthal. Certain key genes, such as those that help Tibetans survive at high altitude, may have come from other species. Neanderthals and Denisovans also interbred with each other.

2) Native Americans almost all descend from a single migration of people from Asia that took place on the order of 15,000 years ago.

3) Agriculture was spread into Europe by a mass migration of farmers from Anatolia, who genetically replaced most of the native foragers. Those farmers contributed the largest share of the genes of modern Europeans. The data for Asia is not as good but so far it looks like the major ethnic groups of East Asia, including Han Chinese, Koreans, and Japanese, are descended from early farmers who spread out from the Yangtze Valley.

4) Modern races formed from the great shake-up spawned by the discovery and spread of agriculture; in the Mesolithic the racial composition of Eurasia was completely different. Around 15,000 years ago the Neolithic farmers of Anatolia and the Neolithic farmers of Iran were as different from each other as Chinese and Welsh are today.

5) In the Bronze Age, the people of the Black Sea steppes spread very widely across Eurasia, making major contributions to the gene pool from Ireland to India. These people presumably spread the Indo-European languages. The details of this process are still not certain, but the fact of population disruptions between 3300 and 2500 BCE is clear. There is a simple statistical test that can show if one population could be the product of two others, and it shows that medieval Europeans could not be descended just from native foragers and Middle Eastern farmers; a third major contribution is needed.

6) European history after the Bronze Age continued to see migration on a large scale. The Bell Beaker invasion of Britain and Ireland around 2200 BCE may have resulted in the replacement of 80% of the population.

7) Genetic studies in Rome suggest that the population was changed by a migrants from the eastern Mediterranean in the late Republic and early empire, then changed again in the late empire by migrants from north of the Alps.

8) Historians have been arguing about how many Anglo-Saxons came to Britain for 200 years, with no result. Was there a mass migration, or just a coup by elite warriors? But now genetics suggest that about 25% of the genes in Britain come from Anglo-Saxon invaders. Even if they were genetically more successful than the natives, this still requires tens of thousands of migrants, and probably more than a hundred thousand.

The discoveries continue to pour in and the science is still getting better by leaps and bounds. We now have the technology to study family relationships as well as group connections, and this will also be a fruitful avenue of research moving forward.

My mind is still blown every time I think about these discoveries, which have opened a huge new window into the past.

Williams Syndrome and Self-Domestication

Williams Syndrome is a strange and rare psychological condition marked by a complete inability to distrust, a sort of anti-paranoia. If you clicked on a link I posted a few weeks ago (Nothing makes sense except in light of inter-individual variation) you may have read a little bit about it. NPR has an interesting article here:

Jessica's daughter, Isabelle, has Williams syndrome, a genetic disorder with a number of symptoms. Children with Williams are often physically small and frequently have developmental delays. But also, kids and adults with Williams love people, and they are literally pathologically trusting. They have no social fear. Researchers theorize that this is probably because of a problem in their limbic system, the part of the brain that regulates emotion. There appears to be a disregulation in one of the chemicals (oxytocin) that signals when to trust and when to distrust. . . .

When Isabelle was younger, she was chronically happy. She smiled at anything. She loved everyone: family, friends, strangers. She reached for them all, and, in return, everyone loved her. Strangers would stop Jessica to tell about how adorably loving Isabelle was.

But as Isabelle got older, the negative side of her trusting nature began to play a larger role. A typical example happened a couple of years ago, when Jessica and her family were spending the day at the beach. Isabelle had been begging Jessica to go to Dairy Queen, and Jessica had been putting her off. Then Isabelle overheard a lady just down the beach.

"She was telling her kids, 'OK, let's go to the Dairy Queen,' " Jessica says. "And so Isabelle went over and got into the lady's van, got in the back seat, buckled up and was waiting to be taken to Dairy Queen with that family."

Jessica had no idea what had happened to Isabelle and was frantically searching for her when the driver of the van approached her and explained that she had been starting her car when she looked up and saw Isabelle's face in the rearview mirror.

The woman, Jessica says, was incredibly angry.

"She said, 'I am a stranger, you know!' " Jessica says. Essentially, the woman blamed Jessica for not keeping closer watch on her daughter -- for neglecting to teach her the importance of not getting into a car with someone she didn’t know. But the reality could not be more different. "It's like, 'My friend, you have no idea,' " Jessica says.

"Self-Domestication" is a theory about why we are different from our Paleolithic ancestors. Those differences include: our heads are less massive and bony, our faces are smaller, our teeth are less robust. There are three main theories about how this happened. Some people say it was climate change at the end of the Ice Age, others changes in diet related to the origin of agriculture and a general increase in plant foods, but right now the hottest idea is self-domestication. The idea comes from the Belyaev Fox Experiment, in which Russian biologist Dmitry Belyaev showed that he could produce all the changes that we see in domesticated animals (shorter faces, floppy ears, spotted coats, etc.) by breeding for one trait, the willingness to be approached and touched by humans.

The differences between us and Paleolithic humans closely parallel those between dogs and wolves; this can be shown mathematically using skull measurement ratios and so on.

Now comes genetic evidence that the genes implicated in Williams Syndrome may also be involved in the changes that make us "anatomically fully modern humans," and that Williams Syndrome can be seen as a sort of "hyper domestication." These are technical articles in genetics, but if you are really curious see here, here, and here.

Besides being trusting, many Williams Syndrome sufferers are retarded, and I've never heard of one being a genius. So if self-domestication is mild Williams Syndrome, does that mean we have gotten less intelligent? It seems possible. Our heads have gotten smaller, and brain size is correlated with intelligence, albeit weakly. Many domesticated animals are stupider than their wild cousins, including cows and horses. But it isn't always true; domestic pigs are still pretty smart and when they go wild they do perfectly fine, even outcompeting truly wild pigs. Border collies are in some ways much smarter than wolves, for example in their ability to understand human language. And this points to one of the more positive findings of this research: the same genetic changes that make us more like Williams Syndrome kids may have increased our linguistic ability.

And even if we have gotten individually a little less smart, that is of course a lot less important than our increased ability to pool our mental resources.

I don't know how seriously to take this. Williams Syndrome has lots of symptoms, some of which are physical, for example weaker hearts and shorter life expectancies. Just because the same genes are involved doesn't mean the processes are really that similar. This research is very new and experimental, flagged as such in the journals.

But this is just so suggestive that I can't resist passing it on. It provides another way to think about how we have changed and are changing and opens up all sorts of questions.

The Genes of Viking-Age Iceland

Studies of the DNA of modern Icelanders show that they are a mix of Scandinavians and people from the British Isles, and also that the sources are skewed by sex:

Studies of mitochondrial DNA (mtDNA) and Y-chromosomes from contemporary Icelanders indicate that 62% of their matrilineal ancestry stems from Scotland and Ireland and 75% of their patrilineal ancestry is Scandinavian

This matches up perfectly with the sagas, which are full of Irish slave women. But experience shows that studies based on modern DNA can be a faulty guide to the past, so this is not unimpeachable evidence about the actual settlement.

In 2018 Sunna Ebenesersdóttir and colleagues published 27 genomes of varying quality from Iceland, all dating to between 900 and 1150 AD. These included people who seemed to be entirely Norse, others who were entirely Celtic, and still others who were a mix of the two, generally confirming the picture from modern DNA. On the graph, squares are male and circles are female, solid color indicates pre-Christian migrants, shading is pre-Christian non-migrant, and fully open is post Christian. (Ireland converted to Christianity in AD 1000.)

More recently the Eurogenes blogger has taken a look at the five highest quality samples and got the results shown above. The big surprise here is the presence of people who look Swedish rather than Norwegian. I am not sure what to make of this, because the written sources having nothing to say about Swedish Vikings in Britain or Ireland. Does it represent movement back and forth between Sweden and Norway, so that some people who came to Ireland from Norway were ethnically Swedish? Or did news about the land to be had for the taking in Ireland reach noble families in Sweden and inspire some of them to load up a ship and make the voyage? Interesting either way.

More Roman Genetics

The blogger at Eurogenes took the data from the Antonio et al. study of 127 genomes from Roman history and created these cool maps. The hotter the color the greater the similarity to the genes of that period in Rome. Above, the Imperial Period, 27 BC to 300 AD. Notice the strong similarity to Syria, Palestine, and Cyprus, indicating migration from the eastern Mediterranean.

Late Antiquity, 300-700 AD. Shifting back toward western Europe, indicating barbarian invaders or other migrants from the west.

And medieval, 700-1600 AD.

The Genetics of Rome, Mesolithic to Modern

Fabulous new data set of 127 genomes from Rome, spanning the Mesolithic to Early Modern periods, has just been published in Science by Margaret Antonio and colleagues. This is not a lot of data for such a big problem, but I think the results are still very interesting.

Period	Dates	# of Genomes	Note
Mesolithic	10,000- 6,000 BC	3	Similar to all of Western Europe
Neolithic	6000-3500 BC	10	Mass influx of Anatolian farmers
Copper Age	3500-2300 BC	3	Rebound of Mesolithic ancestry
Bronze Age	2300-900 BC	0
Iron Age & Republic	900-27 BC	11	First appearance of Steppes ancestry and North African ancestry, varying between individuals. Population resembles modern Mediterranean population
Empire	27 BC to 300 AD	48	Population shifts toward the Middle and Near East, implying an influx of people; ancestry is highly variable between individuals
Late Antiquity	300 to 700 AD	24	Ancestry shifts back toward northern and central Europe, still highly variable
Medieval	700-1600 AD	28	Continued shift toward northern and central Europe, homogenization

Steppes ancestry (= Indo-European invaders) appears much later in Italy than in central Europe, as one would expect, although the data is pretty poor. For me the most striking discoveries come in later periods when the data is actually pretty good. At the height of the empire Romans were genetically much closer to people in the Eastern Mediterranean (Jews, Syrians) than they had been in the Iron Age or would be later. This implies a major influx of people from that region. Then, in the 300-700 period, the population changed to become more like that of Central and Northern Europe, again implying a major influx of people. In both of these periods Romans were highly diverse. After 700 the influx of genes from north of the Alps continued at a lower rate and the population gradually homogenized.

The data is wonderful because it provides real evidence for things one might have expected. During the late Republic the Romans took tens of thousands of slaves in the eastern Mediterranean, and between them and willing migrants enough people moved west to substantially change the Roman population. In the Late Antique period our written records are full of invading European barbarians – Vandals, Goths, Lombards – followed by more waves of invaders like Franks and Normans. These people, too, left their mark. The end result, shown by 50 genomes of the 1700-1900 period, was a population that sits on the scatter plots about half way between Syria and England.

The Eurogenes Blog has a little video that shows you the Roman sample moving around the scatterplot, very clever.

Good popular article at Science Daily.

DNA from a Mass Grave of Crusaders

DNA has been recovered from the skeletons in a burial pit in Lebanon dated by artifacts and radiocarbon to the 13th century, when the nearby Castle of St. Louis was a stronghold of the Crusaders. The men in the pit had all met violent ends. The researchers:

were able to recover DNA from temporal bones and perform whole-genome sequencing to confirm that the men were Crusaders -- quite a feat considering that the bodies had been burned and buried in a warm, humid climate. Both factors cause DNA to degrade.

The researchers weren't expecting the diverse origins of the men. Some were from Spain and Sardinia, four were locals who were probably recruited to fight, and two carried mixed genetics indicating that they were the result of relations between Crusaders and locals.

"Our findings give us an unprecedented view of the ancestry of the people who fought in the Crusader army. And it wasn't just Europeans," said Marc Haber, first author of the study and a postdoctoral fellow at the Wellcome Sanger Institute, in a statement. "We see this exceptional genetic diversity in the Near East during medieval times, with Europeans, Near Easterners, and mixed individuals fighting in the Crusades and living and dying side by side."

Quite interesting.

DNA from a Colonial Pipestem

One of the things I learned doing historical archaeology that has had the biggest impact on how I view the past concerns the invisibility of race. It is very, very hard to tell from archaeology whether any particular site in the US was occupied by blacks or whites. (Or American Indians, once they had taken up European material culture.) Class is immediately visible in the record; archaeologists are really good at telling rich people from poor people. Sometimes regional differences are also pretty clear. But so far as archaeology can tell you, any given cabin in, say, the Chesapeake region of Maryland or Virginia might have occupied by poor blacks or poor whites.

Enter ancient DNA:

Archaeologists often struggle with the challenge of linking historic-period artifact assemblages with specific communities. In particular, small home sites discovered on historic plantations are often difficult to identify as an African American or white tenant house since the material culture appears similar. The discipline also struggles with how to identify the expression of specific West African cultures in their archaeological assemblages. Here, we discuss how DNA was successfully extracted and analyzed from a clay tobacco pipe stem collected from an African American slave quarter in Maryland, USA, and what this information can and cannot reveal about the people present at the site. We successfully identified DNA from a woman, and genome-wide analyses revealed she was closely related to Mende living in present-day Sierra Leone, West Africa. The ability to recover genetic data from personal artifacts now provides archaeologists a viable tool to address questions about communities and ancestral origins. Furthermore, these findings hold the potential to connect living descendants with their ancestors’ homes.

If these techniques ever become affordable for the average archaeological project, a lot might be learned.

A Map of Migrations

Fascinating animated map that shows the movements of populations across western Eurasia beginning in 8,000 BC, based on 1872 individual DNA datasets. I recommend running it with the "cultures" layer turned off; unless you know a lot of obscure archaeological terms this means nothing and even knowing them I found it distracting.

The two big events are the sudden appearance of yellow Anatolian farmers in central Europe around 5000 BC

and the massive influx of red "steppe derived" people in central Europe around 2500 BC.

Kind of awesome, although of course it assumes that we can reliably identify Anatolian farmers or migrants from the steppes; I accept those identifications but not everybody does.

Hybrid Humans

Back in 2010, geneticists announced that a finger bone from Denisova Cave in Russia's Altai Mountains represented a new species of humans. They have been dubbed Denisovans after their discovery place, and genetic studies done since then show that modern Asians carry some of their genes. They visited the cave between 48,000 and 30,000 years ago.

That remarkable discovery inspired archaeologists to redouble their efforts in the cave, and the result has been a haul of several thousand bone fragments, most too small for even the species to be identified from the shape. More than 2,000 fragments were sent to the Max Planck Institute in Germany, one of the top three ancient DNA labs, but even they were unable to find usable material in most of the bones. The did identify one 120,000-year-old toe bone as Neanderthal. Then they got to work on a sliver of arm or leg bone that showed traces of hominid collagen:

Viviane Slon, then a graduate student at the institute, led a search for DNA in the fragment. She began by hunting for a special set of genes found in the fuel-generating factories of the cell, called mitochondria.

Mitochondria carry a set of genes distinct from those of the cell’s nucleus; these genes, unlike those in the nucleus, are inherited solely from the mother.

In 2016, Dr. Slon and her colleagues reported that they had gotten mitochondrial DNA from the mysterious bone fragment, and that it closely matched genetic material from Neanderthals.

The researchers called that individual Denisova 11, and they began searching the bone for nuclear DNA. Fragment by fragment, they began reconstructing the entire genome.

Strangely, only some of the fragments of nuclear DNA matched Neanderthal genes. There was just as much Denisovan DNA in the bone.

“I was wondering, ‘What did I do wrong?’” recalled Dr. Slon, now a postdoctoral researcher at the institute.

In each pair of chromosomes, one came from a Neanderthal, the other from a Denisovan. This individual, she and her colleagues concluded, was a hybrid.

Astonishing: so many thousands of years later, to catch interspecies mating almost in the act. This young woman had a Denisovan father and a Neanderthal mother. The DNA showed that her father was from the local Denisovan clan, related to the other Denisovan specimens that have been identified. Her mother, though, was not closely related to other Neanderthals from the Altai, but to specimens found in Croatia.

In so many ways, the last Ice Age was a fascinating time. Giant mammoths and other strange beasts roamed the icy plains, hunted by saber-toothed cats and dire wolves. Among them wandered small bands of humans of at least three different species, all of them far-travelers who criss-crossed Eurasia as the climate shifted and the herds migrated. On their travels, they must have regularly encountered other kinds of humans. I suspect that our ancient legends of beast men may got back to those times, preserving memories of those meetings. Sometimes, it seems, sex was part of those encounters. What sort we have no idea; perhaps it was all rape. But perhaps some took place when small bands, living at the edge of survival in a decade frigid even by Ice Age standards, or a time of rapid change that ruined their hunting routines, came together to help each other survive.

I foresee a novel about modern human and Denisovan lovers, each the only survivor of his or her band, no language in common, meeting up in a cave refuge and helping each other through winter, slowly learning to trust each other until desire breaks through.

Steppes Genetics

Ancient DNA data is pouring in faster than anyone can keep track of. The latest results focus on central Asia:

For thousands of years the Eurasian steppes have been a centre of human migrations and cultural change. Here we sequence the genomes of 137 ancient humans (about 1× average coverage), covering a period of 4,000 years, to understand the population history of the Eurasian steppes after the Bronze Age migrations. We find that the genetics of the Scythian groups that dominated the Eurasian steppes throughout the Iron Age were highly structured, with diverse origins comprising Late Bronze Age herders, European farmers and southern Siberian hunter-gatherers. Later, Scythians admixed with the eastern steppe nomads who formed the Xiongnu confederations, and moved westward in about the second or third century BC, forming the Hun traditions in the fourth–fifth century AD, and carrying with them plague that was basal to the Justinian plague. These nomads were further admixed with East Asian groups during several short-term khanates in the Medieval period. These historical events transformed the Eurasian steppes from being inhabited by Indo-European speakers of largely West Eurasian ancestry to the mostly Turkic-speaking groups of the present day, who are primarily of East Asian ancestry.

That's just the abstract; I'll report if there is more information in the article, once I find a copy.

Counting the First American Indians

A new genetic study finds that the original Native Americans numbered between 229 and 300, with an average estimate of around 250.

Note that that is an "effective population," which means the number who contributed to the eventual gene pool. Because some of the founders must have died without leaving descendants, or lost all their children, the actual population must have been larger than that. Statisticians argue about the right figure, but nobody thinks it should be more than double the effective population. So if this calculation is right, the vast majority of American Indians in 1492 descended from between 229 and 500 first settlers.

That's actually a pretty big band; I would have thought no more than 150 or so could hang together through the crossing. But 229 to 500 is what the genetic math is saying now.

David Reich, "Who We Are and How We Got Here: Ancient DNA and the New Science of the Human Past"

Friends have been asking me for years if I can recommend a book on the new science of ancient DNA. I have always said, "No, the field is changing too fast." But now there is finally something I can recommend, David Reich's very impressive Who We Are and How We Got Here.

There is not much original in this book, which summarizes the results of ancient DNA studies over the past decade. Reich has been in the thick of those discoveries, first as part of the team that showed Neanderthals and modern humans had interbred, then as the leader of a lab that has read and analyzed a huge amount of DNA. His writing is not great but it is good. You may find some of his technical explanations hard to follow; I did, and have been reading about this stuff for years. My advice is that if you get bogged down in a particular passage, just skip it and go on. If you do that, you should be able to get a huge amount of information out of this book however minimal your background in genetics or statistics.

I have been writing here all along about the big discoveries, which I would say are these:

• Modern humans interbred with Neanderthals, and outside of Africa human genomes are on average 1 to 2 percent Neanderthal.
• Modern humans in East Asia also interbred with another lineage of archaic humans we call Denisovans, although as Reich shows in this book the identity of Denisoavans is a complex story.
• Our modern races are not ancient branches of the human tree, but the result of mixing that has taken place since the origin of agriculture; 20,000 years ago Eurasia was home to a different assortment of races, and the first farmers of Syria were as different, genetically, from those of Iran as Chinese and Welsh are today.
• There are in the Eurasian family tree groups with no clear obvious descendants today, such as "ancestral West Eurasians"; we call these "ghost populations".
• Modern Europeans are descended from three quite different ancient groups: the Paleolithic hunter-gathers of old Europe, the farmers who migrated from the Middle East beginning around 9,000 years ago; and invaders who came in from the Steppes during the Bronze Age.
• The people of India are a mix of an ancient population ("Ancestral South Asians"), farmers who migrated from Iran during the Neolithic, and West Eurasians; the West Eurasian invaders seem to have come in multiple waves beginning in the Bronze Age. As you would expect by looking at people in India, the mixture of West Eurasian ancestry is much greater in the north, but there is some admixture even in the far south. This mixture skews male, indicating that the invaders were majority male, or else that they did their most successful breeding with local women.
• East Asians are a mixture of an ancient Yangtze Valley ghost population, which spread after the invention of agriculture, with numerous other ghost populations, in particular one in the Yellow River Valley; modern Han Chinese originated within the past 5,000 years from a mixture of those two and possibly other groups.

Reich concludes by recapitulating the essay he published in the Times on whether this genetic data confirms or will feed racism. I have wondered why he went out on a limb over these issues, and some of my friends have as well. I can only imagine that he knows or expects that genetic data is going to come out that somebody will think has racist implications, and he wants to get ahead of the curve.

One of the anti-racist points Reich makes in both his book and his Op-Ed is that modern races are all mixtures of ancient races. There are no pure racial types; miscegenation is our legacy and our origin. It is true that some groups have remained relatively pure for the past 3,000 years or so, but compared to the vast sweep of human evolutionary history that just isn't very long.

In other words, the vast movements and upheavals of modern times – migrations, conquests, the rise and fall of empires, the disappearance of old peoples and the appearance of new ones – are not an aberration. The medieval world seems to have experienced a few thousand years or so of comparative stasis and endogamy, leaving us a legacy of people who think they belong to a pure race (Koreans, Japanese, Han Chinese, Germans, Jews, Celts). But that only goes back a certain distance, and we now have the tools to peer back much farther. In that long view, migration and mixing are the human norm.

Genetic Differences between Races are Trivial Compared to those between Men and Women

Geneticist David Reich has a thoughtful article in the Times today about what modern genetics is teaching us about race. He tries hard to hew a middle line between racism and "races are social constructs," and I think he does a pretty good job. But this is what I find interesting:

So how should we prepare for the likelihood that in the coming years, genetic studies will show that many traits are influenced by genetic variations, and that these traits will differ on average across human populations? It will be impossible — indeed, anti-scientific, foolish and absurd — to deny those differences.

For me, a natural response to the challenge is to learn from the example of the biological differences that exist between males and females. The differences between the sexes are far more profound than those that exist among human populations, reflecting more than 100 million years of evolution and adaptation. Males and females differ by huge tracts of genetic material — a Y chromosome that males have and that females don’t, and a second X chromosome that females have and males don’t.

Most everyone accepts that the biological differences between males and females are profound. In addition to anatomical differences, men and women exhibit average differences in size and physical strength. (There are also average differences in temperament and behavior, though there are important unresolved questions about the extent to which these differences are influenced by social expectations and upbringing.)

How do we accommodate the biological differences between men and women? I think the answer is obvious: We should both recognize that genetic differences between males and females exist and we should accord each sex the same freedoms and opportunities regardless of those differences.

Of course that is a lot easier in theory than in practice, but anyway the basic point stands: the only moral position on genetic differences between different human populations is to treat everyone equally well.

Irish Genes

Ross Byrne et al. have just posted the pre-print of a new article on Irish genes, based on studies of the modern population. They find, first of all, that the Irish are clearly distinguishable, genetically, from the rest of Britain; the biggest division in their dataset is between the two islands. The Xes in the diagram above are representations of individual genomes arranged according to variation; the colors represent groupings in the data. You can see that the distance between the genomes, by variation, roughly maps out the British Isles. Note that while southern Britain is a long way from southern Ireland, northern Ireland and western Scotland overlap.

Close-up of northern Britain and Northern Ireland, with marks for two genetic types that were found in both region. This clearly shows mixing of these populations. It does not show, however, when the mixing took place. Some could be early medieval migration from Ireland to Scotland, some from the Scots migration to Ireland in the 16th century (the Ulster plantations), and some from the economic migration of Irish people to Scotland in the 18th and 19th centuries. In this study they used the genomes of people who lived in the same district as their grandparents, to exclude recent mobility, but that doesn't reach far enough back to catch people whose ancestors relocated in 1800 or 1848.

Cladogram showing how the various populations are related to each other. The authors think their data shows a strong "east-west cline," that is, the farther you get from London, the more different people's genes are from those of the bright red Anglo-Saxon heartland.

Note that Orkney is a serious outlier, quite different from England, Scotland, or Ireland. And this is not just because of the Vikings; even excluding their genes, Orkney still stands out.

The authors also found a lot of variation within Ireland. They knew that some of the difference between Dublin and Ulster and the rest of the island would be because of British immigration in recent centuries, so they worked to exclude that contribution from their calculations. The result is a map of variation that, once again, roughly maps out the island. Even more remarkable, it seems to map out the ancient division of Ireland into five kingdoms known as "fifths." So if you exclude Vikings, Ulstermen from Scotland and English who settled Dublin and Waterford, it looks like many families of rural Ireland have been in the same districts for 1,500 years.

The Skeletons of Roopkund Lake, or, Greeks Lost in the Himalayas

Here's a great example of the things that good genetic testing will continue to tell us about mysteries of the past:

The skeletons of Roopkund Lake: Genomic insights into the mysterious identity of ancient Himalayan travelers

Eadaoin Harney, Niraj Rai, Nick Patterson, Kumarasamy Thangaraj, David Reich

The high-altitude lake of Roopkund, situated over 5000 meters above sea level in the Himalayas, remains frozen for almost 11 months out of the year. When it melts, it reveals the skeletons of several hundred ancient individuals, thought to have died during a massive hail storm during the 8th century, A.D. There has been a great deal of speculation about the possible identity of these individuals, but their origins remain enigmatic. We present genome-wide ancient DNA from 17 individuals from the site of Roopkund. We report that these individuals cluster genetically into two distinct groups-consistent with observed morphological variation. Using population genetic analyses, we determine that one group appears to be composed of individuals with broadly South Asian ancestry, characterized by diffuse clustering along the Indian Cline. The second group appears to be of West Eurasian related ancestry, showing affinities with both Greek and Levantine populations.

Spin your scenario for getting a large party of Levantine Greeks to the Himalayas in the 8th century. Were they the descendants of one of Alexander the Great's colonies? Or had they been led east by a visionary who imagined they might find Prester John and persuade him to bring his armies west to free Jerusalem from Muslim rule?

Steppes Invaders, the Indo-European Languages, and the Origin of Origins

Modern genetic studies have confirmed what archaeologists believed in the 19th century: that Europe was invaded in the Bronze Age, around 2500 BCE, by peoples from the eastern European steppes. This invasion was originally postulated to explain the spread of Indo-European languages, and the genetic confirmation of the entry of steppes peoples has now made this view common again.

But wait – where did the steppes invaders come from?

The source culture of the invaders is called Yamnaya, a neolithic culture that dominated the steppes north of the Black Sea between about 3,500 and 2300 BCE. Obviously they didn't spring into existence from nowhere; who were their ancestors?

Now there is a major new genetic study (Mathieson et al. 2017) that offers some insight into the problem. They argue as follows:

Steppe-related ancestry itself can be modeled as a mixture of EHG [Eastern Europe Hunter-Gatherer] -related ancestry, and ancestry related to Upper Palaeolithic hunter-gatherers of the Caucasus (CHG) and the first farmers of northern Iran.

Remember that the Yamnaya culture was Neolithic, which means that they had pottery and practiced some agriculture. Mainly they were pastoralists, moving around a lot and living off their animal herds. They did not invent farming, herding or pottery themselves, but adopted them from the Middle East. Farming was spread into Europe by a massive migration of farmers, and it presumably made it to the steppes in the same way. So both genetically and culturally the steppes people derived in part from the early farming cultures of the Middle East. Most evidence suggests that the spread of farming and farmers happened from Iran through the Caucasus. However, Mathieson et al. complicate the picture:

From present-day Ukraine, our study reports new genome-wide data from five Mesolithic individuals from ~9500-6000 BCE, and 31 Neolithic individuals from ~6000-3500 BCE. On the cline from WHG [West European Hunter Gatherer]- to EHG-related ancestry, the Mesolithic individuals fall towards the East, intermediate between EHG and Mesolithic hunter-gatherers from Sweden. The Neolithic population has a significant difference in ancestry compared to the Mesolithic, with a shift towards WHG. Unexpectedly, one Neolithic individual from Dereivka, which we directly date to 4949-4799 BCE, has entirely NW Anatolian Neolithic-related ancestry.

The pastoralist Bronze Age Yamnaya complex originated on the Eurasian steppe and is a plausible source for the dispersal of steppe-related ancestry into central and western Europe around 2500 BCE. All previously reported Yamnaya individuals were from Samara7 and Kalmykia15 in southwest Russia, and had entirely steppe-related ancestry. Here, we report three Yamnaya individuals from further West – from Ukraine and Bulgaria – and show that while they all have high levels of steppe-related ancestry, one from Ozera in Ukraine and one from Bulgaria (I1917 and Bul4, both dated to ~3000 BCE) have NW Anatolian Neolithic- related admixture, the first evidence of such ancestry in Yamnaya –associated individuals. Two Copper Age individuals (I4110 and I6561, Ukraine Eneolithic) from Dereivka and Alexandria dated to ~3600-3400 BCE (and thus preceding the Yamnaya complex) also have mixtures of steppe- and NW Anatolian Neolithic- related ancestry.

Got that? So while it looks like the Yamnaya culture of the steppes was the source of a major migration west into Europe, the Yamnaya culture included people who had come in the opposite direction, east from Europe out onto the steppes. These were Neolithic farmers who entered Europe from Anatolia around 6500 BCE. This is a small sample to support much in the way of conclusions, but even these few skeletons prove that such movement did occur. There is also now evidence that ancient hunter-gatherers from western Europe contributed genes to the steppes culture, perhaps because they had been driven out of western Europe by Middle Eastern farmers.

None of that changes the basic formula of a Bronze Age migration from the steppes into Europe; the study confirms the existence of a clearly defined "steppe-related ancestry" that can still be identified in modern Europeans. But while that group is genetically distinct from Europe's first farmers, it included some genes from those farmers, as well as many more genes from the farming people of northwest Iran and the Caucasus. It's complicated, making it harder to identify particular genes as deriving from the steppes invaders, the first farmers, or the ancient Hunter-Gatherers.

And now the real question: where did the original Indo-European language come from? Did it derive from an ancient language of the steppes zone, once spoken by Paleolithic hunter-gatherers? Or did it perhaps reach the steppes with migrants from Iran or even Anatolia? Right now the online forums where people argue these questions are burning up with speculations and denunciations. But with genetic data coming out so fast, we should be much better placed to answer them in a few years.

The Bell Beaker Invasion of Britain

I have written here before about the Bell Beaker phenomenon, which spread across western Europe at the very end of the Neolithic period, around 2800 BCE. At this time the use of copper was fairly common, so this is sometimes known as the Copper Age, but in fact most tools and weapons were still stone or bone. The name comes from their distinctive pottery vessels, one of which is above.

The range of the Bell Beaker culture.

Across much of its range Bell Beaker culture seems to be intrusive. In some places it has been found almost entirely in cemeteries, which are next to village settlements that seem completely unchanged. However a case can be made that it emerged from the local culture in two separate places, Portugal and the Netherlands. Archaeologists still argue over which is the Bell Beaker "homeland" and how the two are related, although the latest data seems to show that the beakers of Portugal are older by at least a century. There is also a raging argument about how the culture spread beyond those homelands: invasion or imitation? I reported back in 2015 on genetic data that suggested violent invasion and partial replacement of native populations.

Now there is a much bigger, better study of European DNA in this period, which you can tell is science because the list of authors fills most of the first page. This goes by the name of Olalde et al. The study is based on high-quality DNA profiles from 170 individuals, 100 of them clearly part of the Bell Beaker culture.

The study shows three very interesting things. First of all it shows that before the spread of the Bell Beaker Folk, the Neolithic inhabitants were closely related to each other across the whole Atlantic seaboard from northwestern Spain to northern Scotland. This is the zone of the great Neolithic monuments, and archaeologists have long speculated that these people must have been connected to each other. Now there is genetic data showing that they were related.

The second thing is that the people of the two early Bell Beaker cultures, in Portugal and the Netherlands, were not closely related. So however the culture spread between those two places, it was not by colonization or some other kind of genetic replacement. The Beaker people of the Netherlands had a very high proportion of steppes ancestry, so they originated in the great migration from the Ukraine into the west that probably spread Indo-European languages. The Iberian Beaker folk, on the other hand, had very little steppes ancestry.

The third thing, which is what has gotten the headlines, has to do with the population of Britain and Ireland. The British data is based on 80 skeletons dating to between 3900 and 1200 BCE:

We next investigated the magnitude of population replacement in Britain by modelling Beaker Complex and Bronze Age individuals as a mixture of continental Beaker Complex (using the Oostwoud individuals as a surrogate) and the British Neolithic population. Fig. 3a [above] shows the results of this analysis, ordering individuals by date and showing excess Neolithic ancestry compared to continental Beaker Complex as a baseline. For the earliest individuals (between ~2400–2000 BCE), the Neolithic ancestry excess is highly variable, consistent with migrant communities who were just beginning to mix with the previously established Neolithic population of Britain. During the subsequent Bronze Age we observe less variation among individuals and a modest increase in Neolithic-related ancestry (Fig. 3a), which could represent admixture with persisting populations with high levels of Neolithic-related ancestry (or alternatively incoming continental populations with higher proportions of Neolithic-related ancestry). In either case, our results imply a minimum of 93±2% local population turnover by the Middle Bronze Age. Specifically, for individuals from Britain around 2000 BCE, at least this fraction of their DNA derives from ancestors who at 2500 BCE lived in continental Europe. 

This is only 80 skeletons, and in this period the surviving burials probably skew toward people of high status. But the evidence is stark: Britain's Neolithic inhabitants left few Bronze Age descendants. In the graph above, the oldest individuals are on the left, and later ones on the right; you can see that by the Middle Bronze, after 2000 BCE, the population seems to have settled down around 80% invader.

As I said, that is just one study of 80 people, probably biased toward the elite. But there is another line of evidence that indicates major population change in this period, the Y chromosomes. It has long been known that most modern men of Atlantic Europe have Y chromosomes that fall into the R1b haplogroup. In Ireland and Britain more than 80% of men fall into this clade. So far there is no evidence at all of R1b in Neolithic Britain or Ireland, and the new study confirms this:

An independent line of evidence for population turnover comes from Y-chromosome haplogroup composition: while R1b haplogroups were completely absent in the Neolithic samples (n=25), they represent 95% and 75% of the Y-chromosomes in Beaker Complex-Early Bronze Age and Middle Bronze Age males in Britain, respectively.

Until somebody finds R1b in a Neolithic skeleton, it will be impossible the refute the argument that the Neolithic populations of Britain and Ireland have been largely replaced by invaders.

The arrival of Bell Beakers in Britain and Ireland was an extension of the great migration from the steppes that dramatically changed the population of western Europe and probably replaced most of the languages. However it seems to have been much worse for the invaded than most of this expansion.

As to how the Beaker Folk were able to leave so many descendants, remember what I wrote before about the plague. Up to 10 percent of the skeletons from the source population of Europe's Indo-European invaders, the Yamnaya of Ukraine, had Yersinia pestis in their bones, the bacteria that causes bubonic plague. It seems likely to me that when they spread west they brought the plague with them, and that it caused terrible mortality in populations with no resistance. The invaders would have had some resistance, helping them to take over areas devastated by the plague. If the Beaker Folk brought the plague to Britain and Ireland, that could explain a lot of the later genetic history of the islands.

The Genetic History of Apples

Chinese and European apples have long been thought to be descended from a wild species called Malus sieversii that grows in central Asia, but they are actually quite different. Why?

The team say the finding suggests that modern cultivated apples have their roots in the trees of Kazakhstan, growing to the west of the “Heavenly Mountains” – the Tian Shan.

Previous research has also suggested that these apples were brought westward by traders along the Silk Road. But the trees which took root, either from deliberate planting or from discarded apple cores, did not grow in isolation: they cross-pollinated with wild species in the area. In particular, researchers have said, the European crabapple, whose small, sharp-tasting fruit is used to make cider.

The new study, says Bai, suggests the resulting apples were large – a trait passed on from Malus sieversii – while the crabapple contribution appears to have made the apples firm and tasty.

Indeed the new research suggests about 46% of the genome of modern, domestic apples is likely passed down from M. sieversii plants from Kazakhstan, with 21% from the European crabapple and 33% from uncertain sources. As the trees were subsequently selected and bred by humans, the apples’ traits continued to be refined for larger size, better flavour and firmness.

Chinese apples are also hybrids, and the difference between Chinese and European apples was created mainly by the different local species with which Malus sieversii  interbred. Fascinating.