Ancient DNA, Genetics and Race

UPDATE: Greg Cochrane is doing chapter by chapter discussion of the Reich book so I will just link to his discussion. This week it is the chapter on India.

On the whole, people from North India have more ANI ancestry, while people in southern Indian have more ASI ancestry. The proportions generally range from 80% ANI to 80% ASI. There are actually a few populations that are close to unmixed ANI (Kalash) or unmixed ASI (tribal populations in South India such as Palliyar, Ulladan, Malayan, and Adiyan). Groups that speak Indo-European languages typically have more ANI, while those speaking Dravidian have more ASI. Populations (including castes) with higher social status generally have more ANI ancestry. The Y-chromosome and mtDNA patterns show that ANI contributed a disproportionate fraction of male ancestry, while ASI accounts for the great majority of female ancestry – again, much like Latin America.

The Y chromosome suggests male ancestry in a situation where the male conquerer mates with female conquered tribes.

The Brahmins have the highest proportion of ANI or Indo European genetic material.

I don’t know how many here are interested in this but the new book by David Reich may prove to be as revolutionary as Murray’s “The Bell Curve”.

I’m reading the new book, “Who We Are and How We Got Here”.

It is about ancient DNA which is now being identified and studied. I have been interested in this topic since reading “The 10,000 Year Explosion”, which is about evolution and DNA but it is ten years old. One of the authors, Greg Cochran, has a blog, and has been reading and commenting on the Reich book.

The Denisovans were closer to the Neanderthals than they were to AMH, but not by much. Apparently modern humans split with the common ancestors of Denisovans and Neanderthals about 700,000 years ago, while Neanderthals and Denisovans separated not much later. Almost a trichotomy. Something similar happened when AMH spread into Eurasia: quite early, maybe 50,000 years ago, we split into eastern and western branches. Probably it’s all geography.

AMH is Anatomically Modern Humans.

Another interesting sidelight to this story of how ancient populations moved and replaced forbearers, is the role of Yersinia pestis, the plague organism.

Three pandemics have been attributed to plague in the last 1,500 years. Yersinia pestis caused the third, and its DNA was found in human remains from the second. The Antiqua biovar of Y. pestis may have caused the first pandemic; the other two biovars, Medievalis and Orientalis, may have caused the second and third pandemics, respectively. To test this hypothesis, we designed an original genotyping system based on intergenic spacer sequencing called multiple spacer typing (MST). We found that MST differentiated every biovar in a collection of 36 Y. pestis isolates representative of the three biovars. When MST was applied to dental pulp collected from remains of eight persons who likely died in the first and second pandemics, this system identified original sequences that matched those of Y. pestis Orientalis. These data indicate that Y. pestis caused cases of Justinian plague. The two historical plague pandemics were likely caused by Orientalis-like strains.

Now, the DNA of Y pestis has been found in remains of ancient skeletons, that suggests it might have been responsible for the replacement of ancient farmer by the nomadic Yamnaya people.

The Paleolithic farmers and hunter gatherers were replaced, somewhat like American Indians were replaced by Europeans.The Indians had been isolated from Eurasia for 10,000 years and had lost their immunity and gained no immunity to new diseases that had evolved in the Old World. As a result, they died of diseases like smallpox and measles that they had not been exposed to. The Paleolithic population might have encountered a new disease carried by the invaders from the Steppe.

Late last fall, I reported that scientists had discovered a European ghost population. This group of people then referred to as the ANE, Ancient Northern Europeans, was a previously unknown population from the north that had mixed into the known European populations, the Hunter-Gatherers and the farmers from the Middle East, the Neolithic.

That discovery came as a result of the full genome sequencing of a few ancient specimens, including one from the Altai.

Recently, several papers have been published as a result of ongoing sequencing efforts of another 200 or so ancient specimens. As a result, scientists now believe that this ghost population has been identified as the Yamnaya and that they began a mass migration in different directions, including Europe, about 5,000 years ago. Along with their light skin and brown eyes, they brought along with them their gene(s) for lactose tolerance. So, if you have European heritage and are lactose tolerant, then maybe you can thank your Yamnaya ancestors.

They also had domesticated the horse and used wheeled carts, both huge innovations.

They may have been the ancient Scythians referred to by the Greeks. The preceding population of Europe may have been more easily replaced because they had been victims of Y pestis plague, making an even more ancient example of the power of this organism to change history.

Deep prehistory was always complicated: we just didn’t know much about it before. Ancient DNA analysis is the path forward.

I will add more as I finish the book. He is now discussing the differences between China and India. If anyone is interested, I will do more on this as I finish.

30 thoughts on “Ancient DNA, Genetics and Race”

  1. Yes, please keep going. I have this book and have skimmed through it. What I found interesting were his comments on the Bell Beakers spread across Northern Europe. If it’s true that they adhered to some sort ancient ideology consisting of a pluralistic melting pot, this seems to me like a plausible ancestry of the customs, values, and structures of the Anglosphere.

  2. It’s early days, yet, in all this. I’d pay attention to it, but hold off on making any dramatic pronouncements about what it all means until we actually have all of this crap nailed down.

    One concern I’ve had with much of this work is how focused it is on the genes; I doubt that they are all that goes into “making us, us…”. The cell lines themselves have to have some significance. An analogy I keep coming back to is that the genes are like magnetic tape, back in the day; they record the music. However, the machinery of playback has at least as much to do with the music produced. A set of genes expressed in one cell line may be entirely different when expressed by another line.

    There’s a huge amount we don’t know; chimerism is something that points that out. When you try to transplant organs, you have huge issues with tissue rejection and immune system issues. Yet, a natural chimera has nowhere near those problems, and can reach adulthood with two entirely different cell lines commingled in the same organism. How the hell does that work? We don’t have a damn clue, nor do we know the prevalence of chimerism across the population.

    This fact tells me that we don’t know as much as we think we do; the genes will tell us a lot, but there are considerable unknowns (both known and unknown, themselves) that we have yet to extract from the whole thing.

  3. “hold off on making any dramatic pronouncements about what it all means until we actually have all of this crap nailed down.”

    That will be years. Years I probably don’t have so I am getting the latest edition of Lewin Genes XII. I started Genes VII and then realized I didn’t know enough molecular biology. I was trying to keep up with my students. I was teaching clinical stuff but genetics is the future of medicine.

    Anyway, by the time I got to the end of Albert’s The Cell, Lewin was in edition IX. It is moving so fast that I could not keep up with the rate of information.

    I’m going to have another go. The trouble with genetics is that old editions are not just outdated but some areas are just wrong.

    I highly recommend “The 10,000 Year Explosion” as an introduction to all this.

    If enough are interested, I’ll post more. I am reading Reich’s book anyway. His stuff on India is interesting. The Indo-Europeans got as far as northern India and Pakistan. They probably ended the Indus Valley civilization.

    Their descendants may be the Brahmins as India has kept very intense class separation and the genetics show this. China has been a melting pot and all Han are close genetically.

    The Sardinians, and the Basques, may be the remnants of the original Neolithic farmers.

    The Sardinians, especially, seem to be related to the “Iceman” from the Alps.

  4. Mike – It wasn’t so much wheeled carts. Other people had that. But the Indo-European steppe people had spoked wheels. Previously in most other cultures carts were too heavy to be moved quickly by horses so could not be used as chariots. The light but strong spoked wheel totally changed the nature of war.

    The Mitanni elite were Aryan and Aryan names occur in the Levant. There is some evidence of Aryans in Mesopotamia.

  5. Grurray – The idea of a relationship between the Bell Beaker culture and the “Anglosphere” is complete, total and utter nonsense.

  6. The domestication of the horse is controversial and the Yamnayan people may not have been the first but few carts were found in older sites and the combination of cart and horse might have been their innovation.

  7. Bell Beaker is too historically remote to connect it to England and culture. It’s too easy to pick up chance similarities and make narratives out of them. Our language is descended from PIE. Yet so are French, German, Italian, Greek. Marija Gimbutas had a theory about patriarchal Indo-Europeans overthrowing a settled matriarchal culture. Fun stuff, and not disproven, but neither has much that we have learned supported it, either.

  8. It is not the domestication of the horse that I find interesting, but the partnership with the dog.

  9. The dog was key; all other cases of domestication follow it.

    And, I’m not so sure that the whole thing wasn’t more a case of mutual habituation and domestication. You look at the history of man since the dog, and you can see the same signs of domestication in ourselves that are observable in the dog–Primarily, the retention of juvenile traits in the adult.

    I suspect that the dog/human partnership started out as mutually beneficial habituation to each other, and then progressed from there. A key feature of that is to note that the Neanderthaler apparently did not come equipped for throwing skills–Shoulders apparently weren’t the same as ours, and were not optimized for throwing hard overhand. Because of this, the Neanderthaler remains we have seem to indicate that their hunt technique was to get up close and personal with the game, stab it to death with spears, and suffer the consequences. Notably, we’ve not found much in the way of signs that they had dogs, either, so the supposition that comes naturally is that the anatomically modern humans had something that the dogs wanted, and which the Neanderthalers were unable to supply. My guess is, and you’ll likely laugh, is that it comes down to the fact that AMH populations which the dogs adopted had the ability to throw things for them… So, a key step on the road to human/dog partnership may well have been playing fetch.

    My guess is that the “gamer wolves” that liked playing with humans hung around the camps, and probably brought back the things the humans threw at them to drive them off, and one thing led to another. After gradual habituation, the partnership probably flowed naturally, with humans using dogs in the hunt, and for guard purposes. Likely, both the hunters and the gatherers liked their dogs, one for helping with the hunt and guarding the away camps, and the others for simple guard purposes. If the dogs didn’t help drive off the other predators, they at least gave warning. The dogs probably found it really useful to have human adjuncts, because that gave the mothers and litters of puppies more security when they were at their most vulnerable, and an easy source of food. The opposable thumbs and belly scritches were probably the icing on the cake.

    We ever get a time machine, and can actually check these things, my guess is that the dog/human thing didn’t start out as a “deliberate domestication”. The human side of that transaction would not have had any examples to go by, but once they got their partnership with the dogs going…? Yeah; everything else would flow, starting with the sheep and goats. Who, of course, got herded by the dogs…

    Whole thing is fascinating to discuss. I don’t think we’d be who we are, without the dog to shape us, and that says a hell of a lot. The fact that we can communicate as well as we do across species is telling, but then again, since we sort of share the same niche in the environment, as pursuit hunters, we’re kinda simpatico.

  10. Cats? That has to be an interesting tale as well.

    Intriguing stuff.

    I’m guessing there might have been something else in the Neanderthal-dog relationship beside the shoulder. Dogs don’t care if you through girlie style, side arm or underhand. I can’t guess what it might have been.

    Given the shoulder issue, I’m wondering if this put them at a competitive disadvantage in throwing the spear and how significant that might have been.


  11. The map doesn’t show Doggerland which probably disappeared around the same time as the migration. Depending on the timing, the Yamnaya could have walked to the British (now) Isles.

  12. Remember that ice ages dropped the ocean level so that the English Channel, as well as the Bering Strait, were dry.

    Also, later in Reich’s book which I continue to read, he describes older remains in South America from about 14,000 years ago when ice still blocked Alaska. He speculates than men could have walked down the coast in zones of the coastal shelf now submerged.

    Those remains are older than the Clovis Culture.

    The only human burial that has been directly associated with tools from the Clovis culture included the remains of an infant boy named Anzick-1.[5][6] Researchers from the United States and Europe conducted paleogenetic research on Anzick-1’s ancient nuclear, mitochondrial, and Y-chromosome DNA.[7] The results of these analyses reveal that Anzick-1 is closely related to modern Native American populations, which lends support to the Beringia hypothesis for the peopling of the Americas.[8]

    The distinctive feature of this culture is the spear points that had two faced edges.

  13. From the Wiki article on the Yamnaya culture.

    The earliest remains in Ukraine of a wheeled cart were found in the “Storozhova mohyla” kurgan (Dnipro, Ukraine, excavated by Trenozhkin A.I.) associated with the Yamna culture.

    One the invention of the wheel.

    Although the world’s oldest wheel has been found in Mesopotamia, the earliest images of wheeled carts were found in Poland and elsewhere in the Eurasian steppes. Some have suggested that due to the immense challenge that the invention of the wheel posed to mankind, it probably happened only once, and spread from its place of origin to other parts of the world. However, others believe it developed independently in separate parts of the world at around the same time. For example, The Ljubljana Marshes Wheel is a wooden wheel that was found in the capital of Slovenia in 2002 and was dated to 3150 BC. At present, the birthplace of the wheel is said to be either in Mesopotamia or the Eurasian steppes. Although Mesopotamia has the oldest known wheel, linguistic evidence is used to support the claim that the wheel originated in the Eurasian steppes.

    Potters wheels may have preceded the use with an axle for carts.

  14. If I were in college today, the most interesting field would be Computational Biology.

    Since the late 1990s, computational biology has become an important part of developing emerging technologies for the field of biology.[4] The terms computational biology and evolutionary computation have a similar name, but are not to be confused. Unlike computational biology, evolutionary computation is not concerned with modeling and analyzing biological data. It instead creates algorithms based on the ideas of evolution across species. Sometimes referred to as genetic algorithms, the research of this field can be applied to computational biology. While evolutionary computation is not inherently a part of computational biology, Computational evolutionary biology is a subfield of it.[5]

    Computational biology has been used to help sequence the human genome, create accurate models of the human brain, and assist in modeling biological systems.

    One of my students was interested in pediatric neurology. I gave her some references in the relationship between oxytocin and Autism.

    Like these.

    I hope she followed up. She was very bright.

  15. I love the name of this journal.

    Molecular Psychiatry. At last Psychiatry may escape the 109th century.

    which OXTR single-nucleotide polymorphisms (SNPs) are associated. Thus, a meta-analytic review of extant studies is needed to determine whether OXTR shows association with ASD, and to elucidate which specific SNPs have a significant effect on ASD.

    That is genetics, computational biology and Psychiatry. About time.

    SNPs are mutations.

  16. I take it as one of the basic human traits that we are wanderers and explorers. And that much of that wandering has been done by water, which leaves no traces from ancient times.

    The South American remains that predate Clovis could represent either the walking path, OR a fishing/hunting culture akin to Aleuts that moved by skin boats along the coast eventually getting clear of the ice cap.

    Even in relatively modern times, the Ming dynasty naval expeditions of the early 1400’s that made Columbus and the Vikings look like pikers were not generally known until the late 20th Century.

    Similarly, the peopling of the Pacific islands was a mystery until relatively recent times. Keeping in mind that the Phoenician culture was seafaring traders that went to Cornwall for tin during the Bronze Age, and later founded Carthage, which later conquered Spain before it was in turn conquered by the Romans; the reported discovery of stones in New England with carvings that could be Roman Spain era variants of Punic could indicate that for a short period of time something akin to the later French fur trade could have existed [high value, compact for shipment luxury good] between North America and the late Roman empire, that ended with the fall of the Western Roman empire, as some have posited. It was not until a generation ago that the Viking settlement at L’Anse aux Meadows was confirmed, and this year they have found another one about 400 miles south of L’Anse aux Meadows at Point Rosee. People will go a long, hard way for profit or to settle, and later generations will not remember it.

    Roman trade with India and China is something not considered by most, but there are hoards of Roman coins found in India. The previously undocumented routes are noted in THE ROMAN EMPIRE AND THE INDIAN OCEAN by Raoul McLaughlin which includes detailed explanations of the deleterious effects the trade had on the Imperial economy. We are always learning, and I suspect that we will never know most human movements, both pre-modern and modern, completely.

    If we cannot be sure about explorations and trade after the development of writing, it is sure that we have missed an awful lot about movements before that. I am not claiming primacy in any way for one group or another, but positing that there were multiple ancient migrations, successful and failed, that took place over time. We are just nibbling around the edges of pre-historical events. And that people explore, travel, and invent as part of their very nature. At least those strains of humans that have made it this far.

  17. like this

    Mike K Says: Your comment is awaiting moderation.
    April 8th, 2018 at 10:57 am
    What’s going on with moderation ?

    [I don’t know. The WordPress comment system is persistently buggy. If anyone can recommend a turnkey solution that allows us to continue to host our own comments please email me. Jonathan]

  18. From chapter 5 The Making of Modern Europe

    It turns out that the discredited idea of the “Beaker Folk” was right for Britain, although wrong as an explanation for the spread of the Bell Beaker culture over the European continent as a whole. So it is that ancient DNA data are beginning to provide us with a more nuanced view of how cultures changed in prehistory. Prompted by the ancient DNA results, several archaeologists have speculated to me that the Bell Beaker culture could be viewed as a kind of ancient religion that converted peoples of different backgrounds to a new way of viewing the world, thus serving as an ideological solvent that facilitated the integration and spread of steppe ancestry and culture into central and western Europe. At a Hungarian Bell Beaker site, we found direct evidence that this culture was open to people of diverse ancestries, with individuals buried in a Bell Beaker cultural context having the full range of steppe ancestry from zero to 75 percent (as high as in people associated with the Corded Ware culture)…

    But now we know that these people were linked by major migrations, some of which overwhelmed earlier cultures, providing evidence that these migrations had profound effects. We also need to look again at the spread of language, a direct manifestation of the spread of culture. That almost all Europeans today speak closely related languages is proof that there was strong dissemination of a new culture across Europe at one time.

    And also the Beaker Phenomenon and Spread of Steppe Ancestry to Britain

    Science is science. The recent DNA discoveries have invalidated once and for all those master race theologies that had caused so much trouble in the world. Bell Beakers have been vindicated and are indeed the ancestors of the Anglosphere civilization.

  19. Cochran has a blog thread today about dishonesty about race in this work.

    By the way, there’s something odd and interesting in that early result: why would most of the risk variants all land in one small segment of the genome? But back to the fools: Reich talks about the anthropologists [ Montagu] , geneticists [Lewontin] , and sociologists that have argued that ‘race’ has no biological reality, that there are not really any significant biological differences between races, that research into such differences should be banned ( why is this necessary if differences don’t exist?), etc. All liars, of course. Although I can think of a few people saying similar things that are not liars: they’re just not very bright.

    I’m sympathetic to Reich who obviously does not want tp be treated like Charles Murray.

  20. There are variations, but the essence is a belief that the Aryans founded the great ancient civilizations of the Near East and Mediterranean then moved up to Northern Europe. The people living below the Alps and Carpathians are a mix of Moors, Arabs, Turks, Africans, etc. Jews and Slavs were the ones who came from Central Asia.

    The sanitized versions heard today have to do with so-called European Jews not belonging in the Holy Land; everyone living below Turkey should either accept that they are Arab or should decamp immediately off of land rightfully owned by Arabs; Hungarians, since they really aren’t part of the European race, should welcome being repopulated by their Muslim migrant cousins; modern Greeks living now in Hellas aren’t related to classical Greeks who founded Western Civilization.

    With DNA analysis we now know that it isn’t true. Northern Europeans came from Central Asia. Two subsequent waves of movement united disparate peoples into a pluralistic whole, culminating in the Beakers leading the rabble into Britain.

    Reich doesn’t mention Jews in his book, but other recent studies show Ashkenazi Jews genetically close to indigenous Levantine Christians, Druze, Armenians, Figure 3.
    Palestinians are not. They are related to Saudis, Yemenis, Bedouins, and other Arabs, and they arrived in Israel later. Maybe much later.

  21. @ Gurray – I think you need to look at the chronology of the areas you are discussing. You seem to think that “Long Time Ago” is all the same thing. Also, you seem to be thinking about ancient groups mostly in terms of some modern groups that might be descended from them. It’s all muddled.

    My suggestion would be to start at about 40,000 years ago with a map of current Europe, Mediterranean, and Central Asian. Then move forward a millennia at a time and see what we know or suspect at each spot. It will be a long time before you get to the common era and the dim beginnings of anything that might be called the Anglosphere.

  22. The obvious connection is with the Anglosphere’s Absolute Nuclear Family. Archeological evidence suggests Beaker Folk were different from other Neolithic groups in that they didn’t engage in communal living with extended family. Their settlements were small communities consisting of individual families occupying separate dwellings.

  23. Palestinians are not. They are related to Saudis, Yemenis, Bedouins, and other Arabs, and they arrived in Israel later. Maybe much later.

    More bad news for Palestinians.

    They are the sad sacks of the Middle East.

  24. Here is another update from Greg Cochran on the book.

    His are better summaries than mine and the comments are excellent.

    This is called “Who We Are: #9 Europe”

    I have 100% European DNA with a Y chromosome haplotype derived from Niall of the Nine Hostages.

    The spread of haplogroup R-M222 in northern Ireland and Scotland was likely aided by men like Niall of the Nine Hostages. Perhaps more myth than man, Niall is said to have been a King of Tara in northwestern Ireland in the late 4th century C.E.

    That update is outstanding and more than I could do. Greg Cochran write “The 10,000 Year Explosion” the first good book on genetics ten years ago.

    That is his blog which is a treasure trove of genetics.

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