Razib Khan One-stop-shopping for all of my content

March 23, 2019

Finishing What Darwin Began

Filed under: Books,Culture,Science & Tech — Razib Khan @ 2:30 am
Wilson argues cogently that humanity, both in its biology and its culture, is a product of evolution.

March 22, 2019

Open Thread – Brown Pundits

Filed under: Open Thread — Razib Khan @ 2:18 am

Please keep the other posts on topic. Use this for talking about whatever you want to talk about.

March 20, 2019

The population turnover in westernmost Europe over the last 8,000 years

Filed under: Historical Population Genetics,Spain — Razib Khan @ 7:53 pm


The figure above is from The genomic history of the Iberian Peninsula over the past 8000 years. If you had seen something like this five years ago, you’d be gobsmacked. But today this is not atypical, especially in light of the fact that Spain seems to harbor many good sites in relation to the preservation of ancient DNA. In the figure above you see an excellent representation of the different streams of ancestry and settlement within Spain over the last 8,000 years. You can conclude from it, for example, that only a small proportion of the ancestry of modern Spaniards derives from people who were residents of the peninsula during the Pleistocene. Similarly, you can also conclude that a minority, though non-trivial, proportion of the ancestry of modern-day Spaniards derives from people who arrived during Classical Antiquity and the Moorish period.

And, confirming earlier work, the Basques seem to be relatively untouched by these later gene flow events. To some extent, we all knew that, as the Basques were famously exempt from limpieza de sangre, the blood purity laws of medieval Spain. But importantly, the Basques have a substantial amount of ancestry from peoples whose heritage goes back to Central Europe, and to a great extent, the forest-steppe of far eastern Europe. This is a huge change from what was understood fifteen years ago. As the Basques speak a clearly non-Indo-European language, many scholars hypothesized that they were remnants of hunter-gatherer peoples, who had been resident in the Iberian peninsula since the Pleistocene.

But the reality is that the origin of the Basques is likely in the arrival of Near Eastern farmers. The Basques share a strong genetic affinity with the peoples of Sardinia, who are the closest proxies in modern European populations for this group. Importantly, the Basque difference from Sardinians is their much greater proportion of Central European/steppe-like ancestry. How did they get this ancestry?

One of the major results of this paper is that a particular branch of R1b came to dominate Spain around 4,000 years ago. Before this period the dominant Y chromosomal lineages in the Iberian peninsula were those associated with the farmer populations. The frequency of R1b is above 80% in Basque males. This is one reason that earlier scholarship assumed that R1b was associated with European hunter-gatherers (the Basque being the descendants of those people). Today, we know that both branches of R1 seem to have expanded ~4,000 years ago and that the most common lineages in western and southern Eurasia seem to go back to the steppe peoples.

It may be that the Basque language actually derives from the steppe as non-Indo-European peoples expanded along with the Indo-Europeans, adopting similar cultural habits and characteristics. This is not a crazy position. The Magyars, for example, are not Turkic or Indo-European, but they adopted a lifestyle associated earlier and simultaneously with Turkic and Indo-European pastoralists. But let’s set this possibility aside. Another option is that the Basque descend from one of the post-Cardial cultures of southwest Europe. That is, their language has roots in the dialects of the early Anatolian farmers. Unlike other peoples, they absorbed the influx of Indo-Europeans, and culturally assimilated them.

This too is not crazy. But how might they have absorbed the Indo-Europeans? In the paper above they tentatively argue, from some of their results, that the Indo-European influx was more male than female. There are suggestions that Basque society may have had matrilineal aspects. This does not entail that they were “matriarchal,” but rather, that inheritance passed through the maternal line. Matrilineal societies are not necessary pacific. The Iroquois are a case in point. And, they have a natural way of assimilating warbands of alien males: these men could become integrated into the preexistent kinship networks.

How might the rise of R1b lineages have occurred so fast? One could posit those young men with Indo-European fathers may have had connections to hostile Indo-European tribes that their cousins with non-Indo-European fathers lacked. If the Indo-Europeans were patrilineal, as seems likely, and the proto-Basques were matrilineal, then these men would have been well placed to better protect the cultural integrity and political independence of their maternal heritage through connections of their paternal lineage.

I have an explicit model here: the intermarriage of European trappers in the American West with native women. In many cases, the children of these men would be raised within a native context, and so served as a bridge of sorts. And, there is another analogy: the frequency of R1a is quite high in some non-Indo-European groups in South Asia. It will turn out, I believe, that Southern Europe and India share many similarities, as the Indo-Europeans encountered people in these regions with rich and complex societies.

Several years ago, A recent bottleneck of Y chromosome diversity coincides with a global change in culture, was published. The authors note there was an explosive growth several Y chromosomal lineages, including R1b and R1a, on the order of 4,000 years ago. Recently the evolutionary anthropologist Joe Henrich stated that “Religion is a technology for scaling up human societies.” With this in mind, I will state here that patriarchy is a technology for swallowing up human societies. The distribution of Y chromosomal lineages associated with early Indo-European extends outside of the boundaries of Indo-European languages. In fact, the expansion of I1, concordant with R1b, suggests that non-Indo-European lineages were assimilated into expanding Indo-European groups.

There is, of course, a debate whether this expansion was violent or not. I suggest above a way in which Indo-European lineages, at least by origin, could become pervasive in a non-Indo-European society. But, it does seem to more plausible that more direct forms of marginalization were likely. In a pre-modern environment not far from the Malthusian limit it wouldn’t take much for certain male lineages to replace themselves, while others to die out. The descent from antiquity project in Europe is difficult because there does seem to have been an elite paternal lineage rupture with the fall of Rome. Many modern noble families are traceable to the centuries after the fall of Rome, but none of them clearly are linked to before the fall of Rome. This does not mean that there was a massacre of those lineages, but that elite lineages which lost their rents would quickly lose their status.

I do think what we call war was part of the expansion. But war was likely simply one of the many manifestations of the power of rise of these bands of brothers.

The Insight Show Notes — Season 2, Episode 19: Historical Linguistics

Filed under: Historical Linguistics,Indo-European,Language,Linguistics — Razib Khan @ 3:47 pm

The Insight Show Notes — Season 2, Episode 19: Historical Linguistics

This week on The Insight (Apple Podcasts, Spotify, Stitcher and Google Podcasts) we discuss the historical linguistics Dr. Asya Pereltsvaig. The author of Languages of the World and The Indo-European Controversy, Dr. Pereltsvaig is has been an instructor at several institutions in California and Russia, including Stanford and Santa Clara University.

We get our serious nerd on, especially outside of the normal comfort zone, this week. Do you know what a lexicon is? Or a morpheme? Syntax? If you listen, you will know! There was extensive discussion on such major features of human languages, and how they are informative in inferring linguistic relatedness, which has scaffolded so much of our earlier discussions on genetic relatedness.

There was an extensive exploration of Bayesian phylogenetics, and how it applies to an inference of language relatedness and age (the method is used in genetics as well). Dr. Pereltsvaig talks about why she thinks the results from papers, such as Mapping the origins of the Indo-European language family, are misleading. Basically, she believes that the input of vocabulary is not nearly as informative as something like grammar.

See The Indo-European Controversy for much more on this particular topic!

Speaking of vocabulary, Spencer brought up Swadesh lists. These core words are often preserved, and allow researchers to make broad guesses of relationships (for example, simple number words).

Unfortunately, the plasticity of language probably means that the topology of linguistic family trees is correct, but assigning dates to divergence is always going to be problematic. So to archaeology and genetics, it is. Much of the podcast focused on what we don’t know, and may not be able to know, so that other disciplines may have to pick up the slack.


The Insight Show Notes — Season 2, Episode 19: Historical Linguistics was originally published in Insitome on Medium, where people are continuing the conversation by highlighting and responding to this story.

Society creates god, god does not create society

Filed under: Religion — Razib Khan @ 2:30 pm

Several years ago I read Big Gods: How Religion Transformed Cooperation and Conflict. This was after a long hiatus from reading about the topic of religion from a broad evolutionary perspective. In the 2000s, I read Darwin’s Cathedral: Evolution, Religion, and the Nature of Society, In Gods We Trust: The Evolutionary Landscape of Religion, and A Theory of Religion, to name a few works. These are all very different treatments of religious phenomena, from an evolutionary, cognitive, and economic, perspective respectively. But, they are united by examining religious as a ‘natural’ process, and culture as a reducible and analyzable phenomenon.

This is distinct from what you’d find in “Religious Studies”, a field with a more humanistic and historical perspective. Some of the early practitioners in this field, such as Mircea Eliade, were influenced by perennialism, so the epistemological stance tends to differ from the more positivist and scientific frameworks above.

Several years ago I began to look again at the scientific study of religion due to the work of Ara Norenzayan. He seemed to be fusing the evolutionary and cognitive perspective so as to inform how religion might be adaptively useful on a cultural level through co-option of mental mechanisms. Though not rejecting adaptationism, most cognitive anthropologists did not talk much about selective value of religious phenomena, as opposed the psychological mechanistic origins of supernatural intuitions.

Big Gods was a step forward. The thesis was simple: moralistic high gods were major additions to the prosocial toolkit of humans, allowing for the emergence of complex polities beyond the level of the clan. There were two major ways in which Norenzayan tested this hypothesis. The first was experimentally, by showing that priming subjects with “agents” they were less likely to behave unethically. That is, you didn’t do wrong because an ethical supernatural judge was always watching. The second method was using historical methods looking at the changes across societies over the past 10,000 years. Here there were suggestions that “big gods” preceded the rise of social complexity.

I have expressed some skepticism about the priming research in light of the “replication crisis” in psychology. Now it looks like the second path of analysis may provide different results than Norenzayan’s original thesis. A research group using a large dataset have found that complex societies give rise to moralistic high gods, moralistic high gods don’t give rise to complex societies. Complex societies precede moralizing gods throughout world history:

The origins of religion and of complex societies represent evolutionary puzzles…The ‘moralizing gods’ hypothesis offers a solution to both puzzles by proposing that belief in morally concerned supernatural agents culturally evolved to facilitate cooperation among strangers in large-scale societies…Although previous research has suggested an association between the presence of moralizing gods and social complexity…the relationship between the two is disputed…and attempts to establish causality have been hampered by limitations in the availability of detailed global longitudinal data. To overcome these limitations, here we systematically coded records from 414 societies that span the past 10,000 years from 30 regions around the world, using 51 measures of social complexity and 4 measures of supernatural enforcement of morality. Our analyses not only confirm the association between moralizing gods and social complexity, but also reveal that moralizing gods follow—rather than precede—large increases in social complexity. Contrary to previous predictions…powerful moralizing ‘big gods’ and prosocial supernatural punishment tend to appear only after the emergence of ‘megasocieties’ with populations of more than around one million people. Moralizing gods are not a prerequisite for the evolution of social complexity, but they may help to sustain and expand complex multi-ethnic empires after they have become established. By contrast, rituals that facilitate the standardization of religious traditions across large populations…generally precede the appearance of moralizing gods. This suggests that ritual practices were more important than the particular content of religious belief to the initial rise of social complexity.

The second figure from the paper shows the general trend:

In the first panel you see that social complexity rises, and as it plateaus moralizing gods show up. The second panel shows the distribution of time difference between the emergence of the plateau and moralistic gods across their data set. What’s striking is how soon moralizing gods shows up after the spike in social complexity.

In the ancient world, early Christian writers explicitly asserted that it was not a coincidence that their savior arrived with the rise of the Roman Empire. They contended that a universal religion, Christianity, required a universal empire, Rome. There are two ways you can look at this. First, that the causal arrow is such that social complexity leads to moralizing gods, and that’s that. The former is a necessary condition for the latter. Second, one could suggest that moralizing gods are a cultural adaptation to large complex societies, one of many, that dampen instability and allow for the persistence of those societies. That is, social complexity leads to moralistic gods, who maintain and sustain social complexity. To be frank, I suspect the answer will be closer to the second. But we’ll see.

Another result that was not anticipated I suspect is that ritual religion emerged before moralizing gods. In other words, instead of “Big Gods,” it might be “Big Rules.” With hindsight, I don’t think this is coincidental since cohesive generalizable rules are probably essential for social complexity and winning in inter-group competition. It’s not a surprise that legal codes emerge first in Mesopotamia, where you had the world’s first anonymous urban societies. And rituals lend themselves to mass social movements in public to bind groups. I think it will turn out that moralizing gods were grafted on top of these general rulesets, which allow for coordination, cooperation, and cohesion, so as to increase their import and solidify their necessity due to the connection with supernatural agents, which personalize the sets of rules from on high.

March 18, 2019

Open Thread, 03/18/2019

Filed under: Open Thread — Razib Khan @ 9:04 pm

Going back to finishing Rulers, Religion, and Riches: Why the West Got Rich and the Middle East Did Not. My general attitude so far is that I’m skeptical, but the author presents a plausible thesis. Additionally, the book is worth reading because of its engagement with the whole literature in this area. It’s got a good bibliography you can follow-up.

We had Shadi Hamid on the Brown Pundits podcast. Really appreciate Shadi’s interest in engaging with a diverse array of people. A real intellectual for our time, and unfortunately all too rare in many places these days (I think Shadi should go on the Extremely Offline podcast, even though he is extremely online).

There’s a Fake Outrage Machine on the Right, Also. Basically, they’re trying to get a professor fired for saying in some forum several years ago that cops should be killed. This is egregious, but one of the features of academia, as it is today, is that egregiousness is defended.

Some people are making the analogy to the professor who is under fire at Sarah Lawrence, who wrote an op-ed suggesting there needs to be more intellectual diversity in academia. That’s a pretty weird comparison, but I guess it tells you something. If you are conservative your very existence is scary. If you are on the Left, suggesting people should be killed is scary. But look, there are literal Communists in the academy. No one is demanding they be fired, and unless you add all sorts of caveats being a Communist often means you believe in violent revolution against a class of people. Being liberal in the broad sense is illustrated only when it’s hard, not when it’s easy.

A conservative assault on academia may need to occur, but it shouldn’t be around small things like a professor here and there. Go for the money. That’s the heart. Crazy professors are like stray strands of hair.

The Stanford professor who rejected one of Elizabeth Holmes’ early ideas explains what it was like to watch the rise and fall of Theranos. If you listened to The Dropout, you get the feeling that Dr. Phyllis Gardner was the hero we didn’t deserve. It must have been difficult to watch what has happened over the past 15 years for her. She knew it was fake all along.

Immune Gene Diversity in Archaic and Present-day Humans. Starting to think that the low diversity and population sizes of northern humans were a long-term problem, and one reason they were absorbed by southern modern humans. Not totally sure though.

Jomon genome sheds light on East Asian population history.

Shared polygenetic variation between ASD and ADHD exerts opposite association patterns with educational attainment.

The Scandals of Meritocracy. Virtue vs. competence. Would you rather have a boss who is evil but competent, or good but incompetent? The reality is you have to balance the two. Richard Nixon was probably smarter that Dwight Eisenhower in raw g, but Eisenhower was probably a better person.

Indian population is growing much faster in the north – and the south is paying the price. Much of South India is below replacement. Kerala’s fertility is similar to Japan’s. The Gangetic core of North India is well above replacement. The state of Bihar has 100 million people and a total fertility rate of 3.41. That’s similar to Pakistan’s.

Classic Mechanism of Epigenetic Inheritance Is Rare, Not the Rule. Some geneticists are in “but we all knew that” mode. But the reality is that going by the popular press the public doesn’t know that. The unfortunate reality is that scientific revolutions don’t come around that often.

DNA Friend. Amusing parody site.

Genome-Wide Polygenic Risk Scores and prediction of Gestational Diabetes in South Asian Women.

Fooled By Randomness is my favorite Nassim Taleb book.

Graham Coop has released a textbook, Population and Quantitative Genetics. Since I periodically get emails to delete comments from kids in high school and college, I knew younger people read this weblog. I’d recommend a resource like this to see if you are really interested in population and quantitative genetics.

Check out the Population Genomics blog.

A History of the Iberian Peninsula, as Told by Its Skeletons.

Survival of Late Pleistocene Hunter-Gatherer Ancestry in the Iberian Peninsula.

Population histories of the United States revealed through fine-scale migration and haplotype analysis. White Americans are the garlic people.

BrownCast Podcast episode 24: Shadi Hamid, American politics, Egyptian politics, being online

Filed under: Podcast — Razib Khan @ 5:42 pm

Another BP Podcast is up. You can listen on LibsyniTunes, Spotify,  and Stitcher. Probably the easiest way to keep up the podcast since we don’t have a regular schedule is to subscribe at one of the links above.

You can also support the podcast as a patron (the primary benefit now is that you get the podcasts considerably earlier than everyone else…). Would appreciate more positive reviews.

Today we talk to Shadi Hamid, a Senior Fellow at the Brookings Institution. The author of Islamic Exceptionalism and Temptations of Power.

The range of topics was diverse, from the new live-action Aladin film, the role of religious minorities in Egypt, and what it’s like to seem politically heterodox online. I say seem because Shadi’s sympathies with a sort of Left economic populism that isn’t quite exotic, but he evinces less fixation on epistemological hygiene than is common for modern public intellectuals.

We also talked extensively on his views about the role of religion in life, and religious identity in his own life, and the incentive structures of the careers of D.C. intellectual types.

The evolution of languages

Filed under: Culture,Evolution,Linguistics — Razib Khan @ 2:59 pm
Map of language families of the world today

The story in the Bible about the “Tower of Babel” was the explanation that the ancient Hebrews gave for why there was so much linguistic diversity in the world around them. Ancient people were curious and observant enough to notice that their neighbors did not speak like them. The word “barbarian” comes from the ancient Greek perception of what non-Greeks sounded like to Greeks.

Sometimes linguistic differences can be more subtle, but still critical to life and death. The meaning of the term shibboleth comes out of the context where different ancient Israelite groups pronounced s differently and used that to identify members of an enemy tribe. The limits of your language are often the limits of your tribe.

But evolutionary genetics tells us humans share a common ancestor. That we are one tribe in our genealogy. In fact, the most recent common ancestors of all human populations lived within the last 200,000 years. Outside of Africa, they lived within the last 50,000 years. And, in North and South America it is within the last 15,000 years. We are a young species.

And yet you have a situation such as in the highlands of New Guinea where people who live in different valleys positioned next to each other speak two totally different languages. In North America, Europeans encountered thousands of languages and many language families. And yet we know that most of the ancestors of the natives of North America arrived within the last 15,000 years!

The situation in the Americas may have been the norm in the recent past. Today 40% of the world’s population speak Indo-European languages, but 6,000 years ago it is likely that very few Europeans or Indians spoke Indo-European languages. The spread of English, Arabic, and Chinese occurred in historical time. Their rise to dominance is due to social and political realities of the last 2,000 years.

The ancient world points to incredible linguistic diversity which faded with rising of the “empires of the word.” Over four thousand years ago in Mesopotamia, what is now modern Iraq, many of the people spoke Semitic dialects. Related Arabic and Hebrew. But Sumerian flourished at the time in the south, a language unrelated to any we know of today. In the far north, the people spoke Hurrian, again, a language unrelated to any which flourish today. In the mountains to the east there lived the Guti and Kassites, who seem to have spoken languages unrelated to any spoken today as well.

Etruscans spoke a non-Indo-European language, but influenced the Romans

The Romans record the presence of Etruscans, who influenced their culture, and spoke a language which was not Indo-European. To the further north, there were Ligurians, hugging the coast around modern Genoa, while in the hills there lived tribal Samnites and Oscans. To the south, there were Greek cities and obscure native peoples such as the Sicils. The island of Sardinia was inhabited by speakers of what we now term “Paleo-Sardinian,” perhaps related to Basque. The ancient world was one great Babel.

What this highlights is that while genetic evolution proceeds slowly, gradually, and continuously, linguistic evolution can be riotous, rapid, and proliferate at light speed toward unintelligibility.

Just by physical inspection, one can tell that Finns and Swedes share common ancestors. That they are genetically related. But linguistically they are as different as can be. Finnish is no closer to Swedish phylogenetically than it is to Bantu or Chinese! Swedish as a language is most definitely closer to Bengali, Spanish, or ancient Hittite, than it is to Finnish.

Evolution simply describes a change in characteristics which be defined on a phylogenetic tree. This can be biological, as with genetic evolution, or, it can be cultural. But clearly, the mechanisms matter here. Mendel’s laws impose constraints and regularity to biological evolution which culture lacks. Half of your genetic material comes from each parent. There is no such constraint with culture. In fact, your cultural inheritance may come from someone who is not your biological parent.

Whereas genetic evolution can be traced through modern scientific methods to billions of years in the past, elements of cultural evolution shift so fast that most researchers are skeptical of the possibility of going more than ten thousand years in the past. We have a Neanderthal genome, but it is unlikely we will ever be able to reconstruct the Neanderthal languages (there were certainly many!).

The diversity of languages of North and South America illustrates how a small number of people, perhaps a few thousand genetically, can give rise to thousands of languages hundreds of generations later. The diversity we see around us today in the modern era is but a shadow of what was likely the human norm for most of our species’ history. It is as if a massive process of selection has winnowed down the languages spoken down to a few huge families.

And yet we can still discern similarities across many languages separated by history and large geographical distances. This is most famously illustrated by the “Indo-European” languages.

The affinities between Indian languages and those of Europe were discerned by Sir William Jones in the 18th century. After the fact, the similarities are clear to native speakers. A focus on core words that were more likely to be preserved gave rise to “Swadesh lists.”

Here is the number “nine” in various languages:

Finnish: yhdeksän, Hungarian: szám, Basque: zenbakia, Swedish: nio, Czech: neun, French: neuf, Armenian: inn, Bengali: naẏa, Arabic: tis3a, Turkish: dokuz

Even if you are not a linguist or philologist peculiar similarities may jump out at you (as well as discordances). This is because a large number of languages in that list are Indo-European, and share a common origin within the last ~5,000 years. Paired with them are nearby languages which are non-Indo-European.

It is almost certainly the case that most of those languages above are spoken by people who share ancestors within the last ~50,000 years…but evolution on vocabulary is fast enough that the signal of shared ancestry is lost much faster than in genetic evolution.

This is why many historical linguists focus on grammar, rather than vocabulary. Just going by a list of the number of words within the lexicon you might conclude that English is a Latinate language, like French, Spanish or Italian. But if you look at grammar, it is clear that English is a Germanic language. Vocabulary is something that is easily shared, and quite protean. Consider how quickly different generations develop their own slang and preferred terms.

Grammar is much more conservative, and non-standard speech is often indicative that someone learned English as an adult, and retained the grammar of the language in which they were raised.

Vocabulary evolves fast and responds to selection. People who live in a forested environment may have many ways to describe types of trees. Those who live on a grassland may not. But grammar is part of the deep structure of any language and is evolutionarily conserved. If Noam Chomsky is correct, all grammar is a local expression of “universal grammar,” which is hardwired into our species on the deepest levels.

And yet all of this fascinating research and knowledge is constrained by the fact that most of the world’s languages are disappearing. This mass extinction is happening due to globalization, trade, and the advantages of speaking an ‘international’ language. Of the world’s 7,000 living languages, nearly half are in danger of going extinct.

With the extinction of a language, a peoples’ whole memory fades into oblivion, as well as the record of human diversity from which we can make inferences about the power and range of evolutionary processes in culture.


The evolution of languages was originally published in Insitome on Medium, where people are continuing the conversation by highlighting and responding to this story.

The evolution of languages

Filed under: Diversity,Evolution,Language,Linguistics — Razib Khan @ 2:56 pm
Map of language families of the world today

The story in the Bible about the “Tower of Babel” was the explanation that the ancient Hebrews gave for why there was so much linguistic diversity in the world around them. Ancient people were curious and observant enough to notice that their neighbors did not speak like them. The word “barbarian” comes from the ancient Greek perception of what non-Greeks sounded like to Greeks.

Sometimes linguistic differences can be more subtle, but still critical to life and death. The meaning of the term shibboleth comes out of the context where different ancient Israelite groups pronounced s differently and used that to identify members of an enemy tribe. The limits of your language are often the limits of your tribe.

But evolutionary genetics tells us humans share a common ancestor. That we are one tribe in our genealogy. In fact, the most recent common ancestors of all human populations lived within the last 200,000 years. Outside of Africa, they lived within the last 50,000 years. And, in North and South America it is within the last 15,000 years. We are a young species.

And yet you have a situation such as in the highlands of New Guinea where people who live in different valleys positioned next to each other speak two totally different languages. In North America, Europeans encountered thousands of languages and many language families. And yet we know that most of the ancestors of the natives of North America arrived within the last 15,000 years!

The situation in the Americas may have been the norm in the recent past. Today 40% of the world’s population speak Indo-European languages, but 6,000 years ago it is likely that very few Europeans or Indians spoke Indo-European languages. The spread of English, Arabic, and Chinese occurred in historical time. Their rise to dominance is due to social and political realities of the last 2,000 years.

The ancient world points to incredible linguistic diversity which faded with rising of the “empires of the word.” Over four thousand years ago in Mesopotamia, what is now modern Iraq, many of the people spoke Semitic dialects. Related Arabic and Hebrew. But Sumerian flourished at the time in the south, a language unrelated to any we know of today. In the far north, the people spoke Hurrian, again, a language unrelated to any which flourish today. In the mountains to the east there lived the Guti and Kassites, who seem to have spoken languages unrelated to any spoken today as well.

Etruscans spoke a non-Indo-European language, but influenced the Romans

The Romans record the presence of Etruscans, who influenced their culture, and spoke a language which was not Indo-European. To the further north, there were Ligurians, hugging the coast around modern Genoa, while in the hills there lived tribal Samnites and Oscans. To the south, there were Greek cities and obscure native peoples such as the Sicils. The island of Sardinia was inhabited by speakers of what we now term “Paleo-Sardinian,” perhaps related to Basque. The ancient world was one great Babel.

What this highlights is that while genetic evolution proceeds slowly, gradually, and continuously, linguistic evolution can be riotous, rapid, and proliferate at light speed toward unintelligibility.

Just by physical inspection, one can tell that Finns and Swedes share common ancestors. That they are genetically related. But linguistically they are as different as can be. Finnish is no closer to Swedish phylogenetically than it is to Bantu or Chinese! Swedish as a language is most definitely closer to Bengali, Spanish, or ancient Hittite, than it is to Finnish.

Evolution simply describes a change in characteristics which be defined on a phylogenetic tree. This can be biological, as with genetic evolution, or, it can be cultural. But clearly, the mechanisms matter here. Mendel’s laws impose constraints and regularity to biological evolution which culture lacks. Half of your genetic material comes from each parent. There is no such constraint with culture. In fact, your cultural inheritance may come from someone who is not your biological parent.

Whereas genetic evolution can be traced through modern scientific methods to billions of years in the past, elements of cultural evolution shift so fast that most researchers are skeptical of the possibility of going more than ten thousand years in the past. We have a Neanderthal genome, but it is unlikely we will ever be able to reconstruct the Neanderthal languages (there were certainly many!).

The diversity of languages of North and South America illustrates how a small number of people, perhaps a few thousand genetically, can give rise to thousands of languages hundreds of generations later. The diversity we see around us today in the modern era is but a shadow of what was likely the human norm for most of our species’ history. It is as if a massive process of selection has winnowed down the languages spoken down to a few huge families.

And yet we can still discern similarities across many languages separated by history and large geographical distances. This is most famously illustrated by the “Indo-European” languages.

The affinities between Indian languages and those of Europe were discerned by Sir William Jones in the 18th century. After the fact, the similarities are clear to native speakers. A focus on core words that were more likely to be preserved gave rise to “Swadesh lists.”

Here is the number “nine” in various languages:

Finnish: yhdeksän, Hungarian: szám, Basque: zenbakia, Swedish: nio, Czech: neun, French: neuf, Armenian: inn, Bengali: naẏa, Arabic: tis3a, Turkish: dokuz

Even if you are not a linguist or philologist peculiar similarities may jump out at you (as well as discordances). This is because a large number of languages in that list are Indo-European, and share a common origin within the last ~5,000 years. Paired with them are nearby languages which are non-Indo-European.

It is almost certainly the case that most of those languages above are spoken by people who share ancestors within the last ~50,000 years…but evolution on vocabulary is fast enough that the signal of shared ancestry is lost much faster than in genetic evolution.

This is why many historical linguists focus on grammar, rather than vocabulary. Just going by a list of the number of words within the lexicon you might conclude that English is a Latinate language, like French, Spanish or Italian. But if you look at grammar, it is clear that English is a Germanic language. Vocabulary is something that is easily shared, and quite protean. Consider how quickly different generations develop their own slang and preferred terms.

Grammar is much more conservative, and non-standard speech is often indicative that someone learned English as an adult, and retained the grammar of the language in which they were raised.

Vocabulary evolves fast and responds to selection. People who live in a forested environment may have many ways to describe types of trees. Those who live on a grassland may not. But grammar is part of the deep structure of any language and is evolutionarily conserved. If Noam Chomsky is correct, all grammar is a local expression of “universal grammar,” which is hardwired into our species on the deepest levels.

And yet all of this fascinating research and knowledge is constrained by the fact that most of the world’s languages are disappearing. This mass extinction is happening due to globalization, trade, and the advantages of speaking an ‘international’ language. Of the world’s 7,000 living languages, nearly half are in danger of going extinct.

With the extinction of a language, a peoples’ whole memory fades into oblivion, as well as the record of human diversity from which we can make inferences about the power and range of evolutionary processes in culture.

March 16, 2019

Open Thread – Brown Pundits

Filed under: Open Thread — Razib Khan @ 2:17 am

Please keep the other posts on topic. Use this for talking about whatever you want to talk about.

March 15, 2019

Two phases of Brown Pundits

Filed under: Analytics,Blog — Razib Khan @ 1:03 pm


No idea what happened in Feb of 2018. But that’s when engagement/traffic really went up to a new plateau.

March 14, 2019

The Ubiquitous Sequencing Age

Filed under: Genomics — Razib Khan @ 10:46 pm

Several years ago Yaniv Ehrlich published A Vision for Ubiquitous Sequencing. We’re inching in that direction. In The Atlantic Sarah Zhang has a piece, An Abandoned Baby’s DNA Condemns His Mother, while The New York Times just came out with, Old Rape Kits Finally Got Tested. 64 Attackers Were Convicted:

Still, even with such successes, the problem of untested rape kits persists. Advocates for rape victims estimate that about 250,000 kits remain untested across the country.

Unfortunately, until recently, the ‘forensic genetics’ employed rather primitive 1990s technology. But that’s changing, though both money and expertise need to be brought to bear. Companies such as Gencove and Othram are bringing that expertise to a broader market, with the latter company focusing specifically on the forensic market.

So ubiquitous sequencing is happening. Soon. What does that mean? We need to think about privacy. We need to think about data. We need to reflect on the broader implications of this world beyond specific targeted tasks such as forensic identification.

Open Thread, 03/14/2019

Filed under: Open Thread — Razib Khan @ 12:15 am

Again, recommend Nature’s Metropolis: Chicago and the Great West. Great book.

Creating Christian Marriage in Early Islamic Arabia:

…perhaps the earliest, of a churchman saying definitively that marriage isn’t marriage without a specific Christian ritual comes from an unexpected corner of the late antique world: the Persian Gulf island of Dayrin (modern Tarut in Saudi Arabia) under the rule of the early Muslim caliphate. On this island in 676, Patriarch George I—chief bishop of the Church of the East, one of the two main churches of the Syriac Christian tradition—issued a canon that only unions that received a priestly blessing would be recognized as legitimate, lawful marriage….

…Patriarch George’s writings suggest that East Arabian Christians habitually drank at Jewish taverns and participated in “pagan” funerals—pagan, that is, in their “un-Christian” ostentatiousness. Significantly, interreligious mixing extended into family relations too. George complains of Christian women marrying “pagans,” here meaning Muslims….

I’m not a total revisionist. But not the date. 676. Contrary to traditional Islamic historiography I think it is highly plausible, even probably, that these men would not have been “Muslims” as we’d conceive of them. Rather, Islam, as we’d understand it really, makes sense only from 750 AD and later, with the emergence of the Sunni ulema, the turn against philosophy in mainstream Islam, and the focus on religious legalism. No Bukhari, no Islam.

This brings me to another issue that emerged in a discussion with a reader about Brown Pundits. Some Hindus say that their religion is founded in the Vedas. Similarly, though traditional most Muslims (Shia and Sunni) ground their faith in customs and traditions which accrued organically in the centuries after the death of Muhammad, they will assert that the fundamental basis of their religion goes back to Muhammad and that Islam qua Islam exploded out of the deserts of Arabia under the Rashidun.

From the perspective of the nonbeliever, I think both narratives miss important cultural genealogical features of the development of “Hinduism” and “Islam.” Hindus believe that their religion is the tradition of the Aryans. I hold that the Aryan, Indo-European, traditions that are present within Hinduism are calcified fossils, artifacts which symbolic meaning, but that the core of Dharmic traditions, whether Hindu or Buddhist or Jain, are not fundamentally from the Indo-Europeans. Some intellectual historians suggest that the Sramanic traditions, the counter-Hindu movements, are a revolt of the indigenous non-Aryan components. But I think the same is arguably true of Puranic Hinduism. All of these religions are qualitatively different from the sacrificial ritualism of the pastoralist Aryans.

Similarly, with Islam it is no secret that I am sympathetic with the argument that the emergence of the mawālī, non-Arabs, within Islam after 750 A.D. fundamentally transformed from the religion. Whereas proto-Islam under the Umayyads crystallized was the cult of the ruling caste, an Arab peculiarity, under the Abbasids, who saw the waxing of Iranian culture within the Caliphate, Islam became the religion of the state, and eventually the dominant element of the society. Though I would argue that the influence of Iran and Turan on Islam is probably quantitatively less than that of non-Aryan India on Hinduism, the transformation is great enough that I think one can make a similar case that Islam, a post-Christian Arab ruling sect, was “hijacked” by Iranian and Turanian modalities under the Abbasids.

Again, to be clear, I am not interested in “explaining” to Muslims or Hindus that “actually….” their religion isn’t what they think it is. I’m trying to get a better sense of cultural development and relatedness from the perspective of non-believers.

Biotic interactions affect fitness across latitudes, but only drive local adaptation in the tropics. This surprised me at first blush.

A week ago I had a conversation with Thomas Chatterton Williams for the BrownCast. One thing that we both agreed on: we hate Twitter, but we can’t leave it. Also, lots of people on Twitter are very stupid. I used to think commenters on this blog were stupid, but the reality is that you are geniuses among the dull compared to the Twitter mobs.

Why Elites Dislike Standardized Testing. The reality is that the gains to test-prep are not that great. ETS works really hard on this. But if you read Twitter or many mainstream commentators they act as if test-prep is driving the inequalities. It’s not. The world is full of bullshit.

The Life History of Human Foraging: Cross-Cultural and Individual Variation. Very important paper.

A Bayesian Approach for Inferring the Impact of a Discrete Character on Rates of Continuous-Character Evolution in the Presence of Background Rate Variation. I don’t know much about the details of phylogenetic methods, but the first author is an old grad school classmate of mine. He knows his shit.fopen

Integrating natural history-derived phenomics with comparative genomics to study the genetic architecture of convergent evolution.

Genomic architecture of phenotypic plasticity of complex traits in tetraploid wheat in response to water stress.

March 13, 2019

Siete Habanero Sauce, 4.5 stars out of 5.0

Filed under: Hot Sauce — Razib Khan @ 5:36 pm

Tried out Siete Habanero Hot Sauce today. I really like it!

That being said, I have my biases. I like them hot. It’s moderately hot…it won’t burn a hole through your alimentary system, but it will kick you gently in the mouth. Second, it’s not a very sweet sauce, but a savory one. That makes sense in light of the avocado oil.

But the most exceptional and pleasant aspect of Siete Habanero Hot Sauce is the fact that somehow the spice kicks in later on. Instead of barging in the front door you can taste the creamy avocado before there is a “finish” of habanero spiciness. It’s something I always look for in a hot sauce since it allows for full flavor appreciation.

The Insight Show Notes — Season 2, Episode 18: The genetics of the Irish

Filed under: Genetics,Ireland,St. Patrick's Day — Razib Khan @ 3:47 pm

The Insight Show Notes — Season 2, Episode 18: The genetics of the Irish

The Hill of Tara

This week on The Insight (Apple Podcasts, Stitcher and Google Podcasts) we discuss the genetics of the Irish with Dr. Lara Cassidy. She is a researcher at Trinity College, Dublin, in the Bradley laboratory.

Ireland is an interesting nation because the vast majority of people of Irish descent live outside of Ireland due to migration. So the history of his island is more important than the several millions of modern citizens of Ireland would indicate.

Most of the conversation focused on the Holocene. The last 11,650 years, after the Ice Age and the Paleolithic. But the Pleistocene and the Ice Age framed the discussion because it looks like Ireland, like Britain, was probably not inhabited by humans during this period.

When humans did arrive, they were “western hunter-gatherers” of the Mesolithic. About 6,000 years ago the Neolithic, the New Stone Age, arrived in Ireland with farming. Genetics tells us these were very different populations. With the farmers mostly replacing the hunter-gatherers.

Carnac Megalith

Then 4,500 years ago the Beaker people arrived in Britain and Ireland. These people seem to be genetically very similar to modern Irish and brought a unique culture defined by beaker-shaped vessels.

We also discussed controversies such as the timing of the arrival of the Irish language, and the patterns of interaction across the Atlantic facade, of which Ireland was part (which resulted in features such as the spread of Megalith culture to Ireland from the mainland).

In this context, we explored the Cardial and LBK Neolithic cultures, and how they may have spread to Ireland.

The paper Neolithic and Bronze Age migration to Ireland and establishment of the insular Atlantic genome is a good overview of the patterns we see in Ireland.


The Insight Show Notes — Season 2, Episode 18: The genetics of the Irish was originally published in Insitome on Medium, where people are continuing the conversation by highlighting and responding to this story.

BrownCast Podcast episode 23: Dr. Jeffrey Long on Hinduism, history and politics

Filed under: Podcast — Razib Khan @ 1:17 pm

Another BP Podcast is up. You can listen on LibsyniTunes and Stitcher. Probably the easiest way to keep up the podcast since we don’t have a regular schedule is to subscribe at one of the links above.

You can also support the podcast as a patron (the primary benefit now is that you get the podcasts considerably earlier than everyone else…). Would appreciate more positive reviews.

Today we talk to Jeffrey Long, a professor of religious studies at Elizabethtown College. A practitioner of Vedanta, he is also the author of Historical Dictionary of Hinduism, Jainism: An Introduction, and A Vision for Hinduism: Beyond Hindu Nationalism. Dr. Long is also an editor of Buddhism and Jainism.

We discussed a variety of topics, from the nature of Hindu philosophy, the interaction with Islam, the distinction between astika and nastika schools, as well as Dr. Long’s impressions of Tulsi Gabbard (someone who he actually met at some point).

Swidden rice farming does not lead to high population density

Filed under: Genetics,South Asian Genetics — Razib Khan @ 12:18 am
Admixture on K = 5

I’ve been looking at the data from the recent Munda paper. Standard stuff, admixture, treemix, and f-statistics.The northern Munda samples were collected in Bangladesh. So I thought: I can test the hypothesis that the East Asian ancestry in Bangladesh is to a large part Santhal. After looking at it every which way, I think that in fact, the Munda may not have ever been very populous in much of northeast India. The Santhal is just not a good donor population to Bengalis, at least not when comparing mixes such as Dai + Tamil.

Additionally, the Santhal are really not that well modeled by mixing South Asians with any particular Southeast Asian group, though it works. I think that’s suggestive of the possibility that the Austro-Asiatic group which gave rise to the Munda don’t exist in their current form anywhere in Southeast Asia. Additionally, the Lao samples that are provided in the new paper I think may have Indian ancestry via admixture from Austro-Asiatic Mon or Khmer groups.

Basically, there is so much bidirectional gene flow that I think it’s really hard to get a grip on what’s going on. Additionally, the Burmese and northeast Indian populations (e.g., the Mizos) clearly have a strand of ancestry that derives from relatively recent migrants that came down from the region of eastern Tibet, and perhaps Sichuan or even further north. And this component shows up in Bengalis as well.

On top of this, there is the “Australo-Melanesian” substrate that is present all across Southeast Asia, and probably was present in modern southern China in the early Holocene, which has distant affinities with the “Ancient Ancestral South Indians” (AASI).

At this point, I keep my own counsel. But there may be an interesting story to tell related to how efficient and effective different forms of agriculture were, and how that interplayed with genes and language.

March 12, 2019

Irish memories faded into myth

Filed under: Genetics,History,Ireland,St. Patrick's Day — Razib Khan @ 1:55 pm
Newgrange Neolithic mound site in Ireland

Located on the northwestern fringe of Europe, on the “edge of the world,” Ireland has occupied a special place in the imagination of the West. It was a mild green land beyond the Roman frontier. But it was also near enough at hand that Irish warlords raided Britain, as Romans such as St. Patrick spread Christianity beyond the frontiers of the Empire. There is no Irish Constantine because Ireland converted gradually in the centuries after the fall of Rome. Western civilization arrived in Ireland on its own terms and took on a very local flavor.

But true history begins before Rome. Just because it wasn’t written doesn’t mean that some memory doesn’t persist down to the present. Unlike other peoples of Northern Europe, the Irish have a rich and detailed mythology recollecting the centuries, and perhaps even millennia, before recorded history. Most famously in the Ulster and Fenian Cycles, which tell the tales of ancient heroes such as Cú Chulainn and Fionn mac Cumhaill. But there is also the Book of Invasions, which tells of the origins of the various peoples which contributed to the Irish of the Iron Age.

Today we have archaeology and ancient DNA to supplement the oral memory of the early Irish. Like much of Northern Europe, during Pleistocene Ireland was uninhabited by humans. It was covered by ice.

Rather, humans only arrived during the Mesolithic, as hunter-gatherers seem to have crossed over from the island of British. Because of the separation of the Irish Sea, this means these people had to take to the open waters and travel by boat. This marine barrier also explains the difference, and more restricted, fauna of Ireland in comparison to Britain (which was connected to mainland Europe via Doggerland).

“Bell Beaker”

Ireland before the Iron Age can be divided into three basic epochs defined by tools and lifestyle. First, the Mesolithic, which marks the settlement of Ireland by hunter-gatherers 10,000 years ago, up until 6,000 years ago. Then, the Neolithic, which brought farming to Ireland. This period spans 6,000 to 4,500 years ago. Finally, there is a 2,000 year period when people who worked in Copper and Bronze were dominant in Ireland, eventually to be replaced by the Iron Age cultures which persisted down to the historical period.

These Copper and Bronze Age people seem to have brought a new pottery technique to much of Western Europe. Because of their utilization of bell-shaped beakers, they are termed the “Beaker people.”

With ancient DNA we have clarified some of the genealogical relationships of these populations. It is almost certain that the Mesolithic hunter-gatherers who arrived in Ireland were related to the famous British “Cheddar Man.” Descendents of Pleistocene hunter-gatherers who spread out across Europe after the “Last Glacial Maximum” from southern refuges, genetically they are very similar from Spain in the south to Britain in the north.

Citation: Cassidy et al., 2012

Before ancient DNA it was possible to suggest that farming spread to Ireland through cultural diffusion from the Middle East. Today that is not a feasible position, as an ancient genome from a Neolithic woman who lived more than 5,000 years tells us that in fact, the farmers were a new people. And interestingly, they were not people from whom the modern Irish descended! Rather, these farmers arrived from Southern Europe, and genetically their closest relatives are the modern populations of Sardinia and Iberia.

Newgrange carving

But these Neolithic farmers were not inconsequential in their impact upon the Irish landscape. They were the great megalith builders across Western Europe, and in Ireland were responsible for memorable sites such as at Newgrange. These mounds and ruins were responsible for the emergence of legends about ‘fairy folk’ who lived underground. The farmers had passed into legend and become a myth, their legacy becoming integrated into the sacred landscape of Ireland, even down into the present.

It is only around 2500 BC, with the arrival of the Beaker folk, that the possible ancestors of the current Irish appear on the scene. Though some of the Neolithic people were likely absorbed into the Beaker people, the five centuries before their arrival in Ireland was one of depopulation, as the ancient farming culture collapsed, to be replaced by pastoralism that did not support the cultural complexity that gave rise of Newgrange. The Beaker people may have arrived in a landscape inhabited by ghosts, and the monuments to their past greatness.

But all this leaves many questions still unanswered.

Were the Beaker people speakers of Celtic dialects which gave rise to Gaelic? Or did these people arrive later, during the Iron Age? What were the contributions of various groups such as the Vikings and the Normans over the past 2,000 years? All of these Northern European populations are quite similar genetically, so it is hard to say.

Only time and better techniques will tell.

Interested in learning where your ancestors came from? Check out Regional Ancestry by Insitome to discover various regional migration stories and more!


Irish memories faded into myth was originally published in Insitome on Medium, where people are continuing the conversation by highlighting and responding to this story.

Genes, memes, and Mundas

Filed under: Human Population Genetics,India,Mundas — Razib Khan @ 1:19 am

The Munda languages of the northeastern quadrant of the Indian subcontinent are quite interesting because they are more closely related to the Austro-Asiatic languages of Southeast Asia than to the Indo-Aryan or Dravidian languages which are spoken by their neighbors. The Munda are usually classified as adivasi, which has connotations of being an ‘original inhabitant’ of the Indian subcontinent.

More concretely, the Munda have traditionally operated outside of the bounds of Sanskrit-influenced Hindu civilizations, occupying upland zones and governing themselves as tribal units, rather than being a caste population.

What the field of genetics tells us is that there are really no true aboriginal inhabitants of the Indian subcontinent in an unmixed form. That is, the vast majority of people in the Indian subcontinent have a substantial contribution of ancestry from the wave of migration out of Africa that occupied the southeast fringe of Eurasia beginning ~50-60,000 years ago. The modern adivasi generally are defined more by their social-cultural position within the landscape of Indian culture, as opposed to their long-term residence in the subcontinent.*

The term is a particular misnomer for the Munda because of the evidence that they are intrusive to the subcontinent from Southeast Asia. We have ancient DNA and archaeology which indicates that upland rice farmers, likely Austro-Asiatic, arrived in northern Vietnam ~4,000 years ago. This makes it unlikely to me that they were in India much earlier. The Y chromosomal data indicate that the paternal ancestry of the Munda derives from Southeast Asians, not the other way around.

A new genome-wide analysis of the Southeast Asian fraction of Munda ancestry suggests that it can be as high as ~30%. The paper is The genetic legacy of continental scale admixture in Indian Austroasiatic speakers:

Surrounded by speakers of Indo-European, Dravidian and Tibeto-Burman languages, around 11 million Munda (a branch of Austroasiatic language family) speakers live in the densely populated and genetically diverse South Asia. Their genetic makeup holds components characteristic of South Asians as well as Southeast Asians. The admixture time between these components has been previously estimated on the basis of archaeology, linguistics and uniparental markers. Using genome-wide genotype data of 102 Munda speakers and contextual data from South and Southeast Asia, we retrieved admixture dates between 2000–3800 years ago for different populations of Munda. The best modern proxies for the source populations for the admixture with proportions 0.29/0.71 are Lao people from Laos and Dravidian speakers from Kerala in India. The South Asian population(s), with whom the incoming Southeast Asians intermixed, had a smaller proportion of West Eurasian genetic component than contemporary proxies. Somewhat surprisingly Malaysian Peninsular tribes rather than the geographically closer Austroasiatic languages speakers like Vietnamese and Cambodians show highest sharing of IBD segments with the Munda. In addition, we affirmed that the grouping of the Munda speakers into North and South Munda based on linguistics is in concordance with genome-wide data.

The paper already came out as a preprint many months back, so I’ve already mentioned it. The big finding, to me, is that it uses genome-wide methods to estimate an admixture in the range of ~4,000 between the southern Munda Southeast Asian and South Asian ancestral components. It also confirms something that has been pretty evident for nearly ten years of genome-wide analysis of South Asian population genetics: the Munda have less West Eurasian ancestry even after you account for the Southeast Asian admixture than any mainland Indian population outside of the Tibeto-Burman fringe.

In Narasimhan et al. the authors present a model that fits the data where:

  1. The proto-Munda mix with an “Ancient Ancestral South Indian” (AASI) population that has no West Eurasian admixture in India’s northeast
  2. Then, mix more with an “Ancestral South Indian” (ASI) population that has some West Eurasian admixture

The authors in this paper are skeptical of this model because they have a data set of northern and southern Munda groups, who differ in their Southeast Asian ancestry, but not the ratio of West to South Asian ancestry quanta. The implication here is that Southeast Asian ancestral groups were mixing into a substrate of relatively even West and South Asian admixture, and not one of population structure and clinal variation. And yet the authors are very tentative, and I think they know that resolution is going to come with more data. Their own work indicates for example that the northern Munda have been subject to more gene flow from their neighbors than the southern Munda, so the demographic history could be quite complex.

But a fact I want to highlight is that in a sample of ~900 Munda the fraction of R1a1a, which is presumed by many to be a marker associated with Indo-Aryans, is quite low, at 5%. Mind you, that the Southeast Asian haplogroup is found at more than 50% representation in the Munda, while their mtDNA is almost all deeply South Asian (so ~30% Southeast Asian is reasonable genome-wide). I have long believed that this is indicative of the fact that the modern Munda descend from a patrilocal cultural group which managed to maintain their integrity down the present, as evidenced by their unique languages and mythologies, as well as folkways which have traditionally set them outside of the Indian caste system.

The early Indian legends speak of forest-dwelling tribes, which operate somewhat outside of the domain of agro-pastoralist civilization. Some of these were almost certain the swidden rice cultivating ancestors of the Munda.

The ALDER admixture dates in the paper above probably indicate a slightly later admixture from the true overall one (more precisely it will pick up the last admixture). Additionally, there is no reason it has to be India proper. The ancestors of the Andamanese probably arrived from what is today southern Burma, and so AASI-like people certainly existed in mainland Southeast Asia as part of the Australo-Melanesian continuum which extended out to Oceania.

More details will be forthcoming with more ancient DNA. Rather, I want to suggest here the critical issue of how we relate genes to culture. Or, more poetically, genes to memes. Both the Indo-Aryans and Munda seem to have been male-mediated migrations which brought a distinctive memetic package to the Indian subcontinent, while at the same time not contributing the preponderance of genes to their cultural heirs. Though more than four out of five people in the Indian subcontinent speak Indo-Aryan languages, which likely derive from the speech of agro-pastoralists with roots on the Eurasian steppe, probably closer to one of ten of the ancestors of modern South Asians 4,000 years ago were residents of the said steppe.**

And yet the complexity here defies simple attempts to model how ancestry and culture interact and refract down the generations. I am quite convinced that much of the original Austro-Asiatic rice farmer ancestry of the Vietnamese has been diluted by gene flow from southern China during the period when the region was under Chinese imperial rule. And yet the Austro-Asiatic language persisted. Both the Vietnamese and Munda maintain linguistic connections to ancestors who may not contribute to the dominant proportion of the ancestry to the people who continue their linguistic tradition. In the case of the Munda, this was due to demic diffusion into a landscape where they took the daughters of local peoples as wives, while in Vietnam it was probably continuous gene flow from southern China.

It’s hard to put together a hard and fast list of heuristics to infer past history from extant data. To some extent, there needs to be model building, in addition to making inferences. That being said, it is rather clear now that the period between 5000 BC and 1000 BC seems to be one where we are witnessing several instances of distinct admixture between very different ancestral streams. The latest work from the Reich group confirms the intuition by many of us looking impressionistically at clustering results that there are several layers of West Eurasian admixture within South Asia, and, that those admixtures occurred at different times and different places. Additionally, the genetic data are now in alignment with archaeological and linguistic evidence of the expansion of swidden rice farming people out of the fringe of what is today southern China into South and Southeast Asia.

It is now possible to still suppose that a distinct West Eurasian component was present in northwest South Asia, in the valley of the Indus, as far back as the Pleistocene. And, that this element was mixed in the later Holocene with an ancestral component dominant beyond the Thar desert, with affinities to the south and east. This would preserve the possibility of “Out of India” that some are still holding to. Or at least some sort of broader proto-Indo-European network that spanned more than half of Eurasia. But I think a more parsimonious explanation is that rather than deep local structure within South Asia, agricultural populations migrated from both the west and east, and assimilated the deeply entrenched local substrate.

More thorough ancient DNA temporal transects will tell the tale. As with many empirical questions I’m rather patient about waiting on data to make final conclusions, in part because I have high confidence that we’ve been swimming in the right direction. But you could always be wrong!

* This is in contrast to aboriginal groups in European settler nations, who have precedence as inhabitants of the land, and also organize themselves politically somewhat independently and maintain cultural distinctiveness.

** The methods in the latest preprints give somewhat higher figures, but I heard that they were going to go lower. Additionally, it doesn’t change my qualitative point that most of the ancestry is not from Bronze Age Indo-Aryans.

March 11, 2019

Minding the base rate fallacy

Filed under: Base rate fallacy,Statistical Genetics — Razib Khan @ 8:53 pm

In the near future, I’m pretty sure that most pregnancies will begin with a non-invasive genomic analysis (OK, that’s now they will begin, but you get what I’m saying). Far more extensive than what you get now no doubt.

But, non-invasive prenatal tests (NIPT) is already ubiquitous for a variety of conditions, in particular, those that result in visible changes in the karyotype. Down syndrome is probably the most well-known instance of this, though there are others. Denmark funds NIPT through public monies, and Down syndrome has almost disappeared among children born.

With all that being said, the presentation of results from these tests must be accompanied by some statistical scaffold or primer. Here is a post from someone with a background in computational genetics, How I learned to stop worrying and love Bayes’ Theorem:

At my 9 week doctor’s appointment, my doctor brought up the option of genetic testing, specifically non-invasive prenatal DNA testing. As a geneticist doing bioinformatics, I thought how cool it is that we can test for chromosomal abnormalities from the blood of the mother. The idea is that there are fetal DNA floating around in the mother’s blood and so inferences about whether there is an excess of a particular chromosome can be made by examining the mother’s blood…

Fast forward 2 weeks, I was at a FedEx store faxing my medical record to the doctor’s office at UCLA (I was in Boston for an internship for a few weeks during my first trimester) when I got a phone call from my doctor in Boston. This was the most difficult phone conversation I have ever had in my life. Over the phone, she told me that the NIPT test came back that my baby was high risk (40% chance) for Trisomy 13 (or Patau’s syndrome). My heart dropped….

Some of you see the title of this post. And you see the title of the post I linked to. So you know the conclusion and the moral of the story.

If you are still confused, please do read the post, and afterward please do repeat the phrase “base rate fallacy” to yourself multiple times, because it will prevent you from getting confused. It’s in the class of “news we’ll need to use” in the near future.

Older Posts »

Powered by WordPress