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

October 21, 2018

Open Thread, 10/21/2018

Filed under: Open Thread — Razib Khan @ 11:20 pm

You may have noticed I haven’t been posting much. Busy with other things, like ASHG, work, family, etc. I don’t normally post “won’t be posting often” notices, as no one really cares much about blogs…but when I go into lower production mode people sometimes worry. No reason to worry.

Tim Blanning’s Frederick the Great: King of Prussia is an excellent book. So is The Pursuit of Glory: The Five Revolutions that Made Modern Europe: 1648-1815. Finally, Iron Kingdom: The Rise and Downfall of Prussia, 1600–1947. One of the most interesting things about Frederick the Great: King of Prussia is how Blanning recounts the importance of personally playing and repeatedly listening to music in the life of the German monarch. He was apparently a very competent flutist.

There was talk about ASHG about the Amy Harmon article, Why White Supremacists Are Chugging Milk (and Why Geneticists Are Alarmed). It seems most of the geneticists I know personally were contacted by Harmon at some point over the last two years. A lot of work went into this. Many of our quotes were obviously not used. That’s called journalism.

There was a period when many frog-Nazis were on Twitter brandishing a particular STRUCTURE bar plot (since frog-Nazism has been severely purged by Twitter I see this far less often). I understand that many journalists and people of the “chattering-thinking” classes are strongly influenced by what they see on Twitter in terms of their perception of what’s going on in the world.

Additionally, to be honest for many white people racism is somewhat an abstraction. They need to make recourse to instrumental variables. The SNL election night sketch which shows white liberals talking about how it’s never been so bad, and black comedians nodding along, illustrates a real trend, and that is that many white liberals feel like there has been a massive upsurge of racism over the past few years.* But as a nonwhite person who has lived in this country since the early 1980s, it is clear that America is far less racist than it was back then, and our society has been defined by a gradual decrease in racial prejudice. White support for laws banning interracial marriage went from about 25% in the 1980s to 10% in 2002, when the question stopped being asked because it was such a marginal viewpoint.

A story about the social and political of implications evolutionary population genetics is a reasonable one. And, it might make a somewhat interesting academic paper as well. But the prominence of this piece to me cuts to a deep disagreement about the nature of racial conflict and difference within human societies. Immanuel Kant’s abstract and intellectual reflections on race may be alarmingly white supremacist to many moderns, but the profitable character of exploitation of sugar and the utility of slavery in the West Indies, and the rise of the West in a much more robust manner as signified by the McCartney Mission in the 1790s, was far more important in shaping the emergence of a very vigorous white supremacist ideology in the late 19th century which culminated in Madison Grant and Lothrop Stoddard.

I enjoy discourses on the intersection of race and genetics as much as the next person. I write them myself. But the most concrete thing I can do for the “racial question” is what I’m doing already: participating in the amalgamation of very distinct pedigrees and producing Americans related to a much larger fraction of the world’s population. White Americans who believe in the cause of racial social justice and anti-racism can do something very easily if they so choose: select a non-white partner and produce mixed children. If you are already partnered up, encourage your children to do so. This will make a bigger difference than retweeting how great diversity is, while not living it in your own life. For white progressives, do understand that your nonwhite allies notice the overwhelming pallor of the types of people who become and remain your intimates. You spend an afternoon on a racially diverse panel. Why not spend life in a racially diverse manner? Because I am a political outsider to these issues nonwhites probably feel more comfortable telling me how they perceive you don’t have much skin in the game. An ounce of action is worth a pound of talk (also, you can proactively give money to nonwhite people from your own disposable income).

The above is not a troll at all. I’m not the sort of person who thinks that the type of person another human being becomes friends with, or partners with, is my business. Do as you wish. But if you accept the premises of most forms of anti-racist talk, then Norman Podhoretz’s 1963 essay which enjoins action still applies.

The Uralic podcast is up. Brown Pundits now have a podcast.

This Elizabeth Warren fact-check by the Daily Caller Foundation’s Emily Larsen is pretty good. Having to listen to political pundits talk about ancestry testing all week has been painful. More need for education….

ASHG photo that I find most amusing.

As most of you probably know, the human genome still has gaps. I felt this year more people talked about those gaps, and how to fill them in. Also, lots of African genetics (this was by plan).

May write some more tutorials soon. Depends on the time.

The Slow Burn podcast ended with talking about Juanita Broderick. The Broderick allegations really have shot into prominence over the last few years. But if the Republicans knew about them in detail, that does make their determination to impeach Bill Clinton far more comprehensible.

I don’t have much to say about the Khashoggi thing you haven’t heard elsewhere.

A new analysis of CEU mutation rates is there is an age effect, most mutations are paternal, and, there might be variation in increases in mutations with older individuals by family.

* Most of my white friends tend to point to particular media anecdotes. As a nonwhite person I have not perceived any difference, and I travel in various parts of the country. Your experience may vary.

October 17, 2018

The Insight Show Notes — Season 2, Episode 4: Finnish Genetics

Filed under: science — Razib Khan @ 11:02 am

The Insight Show Notes — Season 2, Episode 4: Finnish Genetics

Midsummer in Finland

This week on The Insight (Apple Podcasts, Stitcher and Google Play) we discussed the prehistory and genetics of the Uralic peoples, with a particular focus on the people of Finland, who are among their most numerous exemplars.

We mentioned that the Uralic languages have a northern distribution, extending from north-central Siberia to northern Europe.

See for yourself:

We mention two recent papers of interest:

We discussed the past 20 years of debate on the origin of the TAT-C/N1c Y chromosomal haplogroup. This male lineage is found at high frequencies all across the northern fringe of Eurasia, and in particular among Uralic populations.

Here is an early paper on the topic: Genetic relationships of Asians and Northern Europeans, revealed by Y-chromosomal DNA analysis. If you want to know the origin of the name “TAT-C”, listen to the podcast! Spencer tells you.

There was a lot of discussion about Uralic culture. For example Kalevala and blood sausage. The eastern Baltic was also one region where farmers from Anatolia never migrated. See The genetic prehistory of the Baltic Sea region.

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

The Insight Show Notes — Season 2, Episode 4: Finnish Genetics was originally published in Insitome on Medium, where people are continuing the conversation by highlighting and responding to this story.

The expansion of the polar people

Filed under: Finland,History,science — Razib Khan @ 10:58 am

The expansion of the polar people

Sami in the far north of Europe

Since the development of agriculture 12,000 years ago, the cultural and genetic landscape of our world has been transformed by the emergence of peasants as the dominant demographic. For most of the recorded history, the average human was a peasant; a laboring tiller of the soil.

There were of course exceptions. Some peoples took up pastoralism. Others specialized in extracting resources from the sea — such as fisherman. And of course, there were hunter-gatherers who continued to practice a lifestyle as old as the human race itself.

Muskox in the Taimyr Peninsula

Though we often think of hunter-gatherers in a tropical context, the reality is that some of the most successful practitioners of this lifestyle have flourished in and around the Arctic. Not only have they flourished, but they have vastly expanded! For instance, the Thule culture of North America famously replaced the Norse agriculturalists of Greenland in the 15th century.

But perhaps the most speculator expansion of a non-agriculturalists in the north has been that of the Uralic peoples. A paper titled “Genes reveal traces of common recent demographic history for most of the Uralic-speaking populations” has an excellent map which illustrates the geographic span of this language family:

Citation: Tambets, Kristiina, et al. “Genes reveal traces of common recent demographic history for most of the Uralic-speaking populations.” Genome biology 19.1 (2018): 139.

Over twenty years ago researchers noted that one particular Y haplogroup lineage, N1c, was very common among Uralic peoples. Notice the overlap in distribution between this lineage and the Uralic populations below.

Distribution of N1c

The question then emerges: did the Uralic peoples come from the east, into northern Europe, or were they indigenous to northern Europe and expanded eastward? Examining patterns of genetic diversity indicate that this Y chromosomal lineage emerged in Siberia and later spread to northern Europe. Why? Because diversity accumulates in regions where the lineage has been present the longest.

Citation: Lamnidis, Thiseas Christos, et al. “Ancient Fennoscandian genomes reveal origin and spread of Siberian ancestry in Europe.” bioRxiv (2018): 285437.

New research from ancient DNA has clarified the timing of the arrival of these Siberians, Ancient Fennoscandian genomes reveal origin and spread of Siberian ancestry in Europe.

What we do know from modern genetic variation is that the Uralic people, including the Finns, seem to have recent Siberian affinities. In contrast, most other Northern Europeans do not have this — making it even more distinct. This Siberian affinity is strongest in the Sami hunter-gatherers of the far north.

Samples from a population in the Kola Peninsula of northern Russia from to 3,500 years ago yielded individuals who were even more Siberian than the Sami — as you can see in the admixture plot to the left. In particular, the Siberian ancestry of the Finnic people seems to be similar to that of the Ngananasn people of the Taymyr peninsula in Russia.

Looking at patterns within the genome of these ancient people, researchers have concluded that these people are the product of mixing between Siberians and indigenous European hunter-gatherers, which began to occur ~4,000 years ago. This aligns with other work that suggests that the Ceramic Comb Culture, the dominant Mesolithic hunter-gatherer society of northeast Europe before the expansion of agriculture, lacked Siberian ancestry.

Nenet Samoyed people

Where does this leave us? If we use genetics as a guide, it seems that around ~4,000 years ago a migration of Arctic hunter-gatherers swept out of the northern fringe of Siberia to the west. These people were likely related to the easternmost of modern Uralic peoples: the Samoyed tribes. The Y chromosomes of western Uralic peoples, such as the Sami and Finn, carry the hallmarks of ancestry similar to the Samoyeds. But the mitochondrial lineage is almost wholly similar to their European neighbors. Therefore, it seems that the spread of Uralic languages westward was due to the migration of males.

One of the implications of these conclusions is that the Uralic languages may have arrived in the Baltic after the Indo-European languages! In much of Estonia and southern Finland, the Corded Ware culture, presumed to be associated with Indo-Europeans, predates 2000 BC by centuries.

Though we often imagine that history and culture move in a singular direction, toward agriculture, the Uralic people may be an instance of an exception. If it is correct that hunter-gatherer Siberian men moved into large areas of northeastern Europe, and culturally assimilated more numerous peoples, some of whom were agriculturalists, it may indicate that the trajectory of history is more winding and complex than we may imagine.

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

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

October 16, 2018

Open Thread – Brown Pundits

Filed under: Open Thead,Open Thread — Razib Khan @ 12:24 pm

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

October 15, 2018

Elizabeth Warren carries Native American DNA – she’s running!

Filed under: Uncategorized — Razib Khan @ 3:19 am

Since I’ve talked about this issue before, Warren releases results of DNA test:

There were five parts of Warren’s DNA that signaled she had a Native American ancestor, according to the report. The largest piece of Native American DNA was found on her 10th chromosome, according to the report. Each human has 23 pairs of chromosomes.

“It really stood out,” said Bustamante in an interview. “We found five segments, and that long segment was pretty significant. It tells us about one ancestor, and we can’t rule out more ancestors.”

He added: “We are confident it is not an error.”

The proportion of ancestry is not large. But it is clearly there. They compared to the Utah white and British European 1000 Genomes populations, which is a good standard for Old Stock Anglo-Americans. She’s clealry an outlier, with about an order of magnitude more “Native American” ancestry. So it’s unlikely to be some artifact.

There is some talk in the article about lack of reference populations. But remember, the key is to identify Native American ancestry, so all of this should coalesce back 10-15,000 years ago. Compared to the divergence from Northern Europeans, this is going to jump out against the genetic background.

So does Elizabeth Warren have Native American ancestry? 99% sure that that is a yes. Is she going to run? Well, I wouldn’t say 99%, but that seems likely too….

(I doubt she’ll do it, but it would be neat if she released her raw results)

Open Thread, 10/15/2018

Filed under: Open Thread — Razib Khan @ 1:16 am

I pinned the above chart to my Twitter profile because I’m “trying to make it happen.” It was David Mittelman’s idea, and the data was courtesy of ISOGG, but putting it together as a graph has really brought home to people how the consumer genomic landscape has changed over the last half a decade.

The plot to the right, which shows a smoothed chart of the total number of kits over time, is also important.

I recorded a podcast for the Urbane Cowboys last week. It should go up today, so watch for it. I talked about a variety of topics, so I don’t know how it will drop in regards to editing.

Was talking to a friend about the importance of emotion in reasoning, or at least how emotion allows us to reason better. He asked about books, and Descartes’ Error came to mind. But I’ve read about critiques of its interpretation of the history of science and philosophy, though I think the big picture conclusion is probably still valid.

Will be at ASHG this week. Mostly I’m going to learn more about African genomics. Not as much on pop-gen as in previous years. If I approach your poster, don’t worry that I’m going to tweet or write about. Just be cool.

Noticed Tim Blanning’s massive survey of Frederick the Great is now less than $10 on Kindle. Because of the World Wars, I think we learn a lot less about Prussia from 1700 on than we otherwise would. Blanning’s The Pursuit of Glory: The Five Revolutions that Made Modern Europe: 1648-1815 is also excellent.

I’m listening to John Keegan’s A History of Warfare on Audible. To be honest I think I’m much better at reading than listening. This should be surprising. In courses, I generally prefer to learn from the textbook as opposed to listening to lectures. And I have a lot of experience reading over my lifetime. Less so listening.

Xuzi: The Complete Text has been a difficult read for me. I’ve gone back and reread passages several times. It is definitely on the discursive side. That being said, I have come to a strange observation: Xunzi’s view of religion is strangely similar to Ludwig Wittgenstein’s. Here from the Stanford Encylopedia of Religion:

He opposed interpretations of religion that emphasize doctrine or philosophical arguments intended to prove God’s existence, but was greatly drawn to religious rituals and symbols, and considered becoming a priest. He likened the ritual of religion to a great gesture, as when one kisses a photograph. This is not based on the false belief that the person in the photograph will feel the kiss or return it, nor is it based on any other belief. Neither is the kiss just a substitute for a particular phrase, like “I love you.” Like the kiss, religious activity does express an attitude, but it is not just the expression of an attitude in the sense that several other forms of expression might do just as well….

This seems similar to Xunzi’s belief that religious rituals were an important part of life, even if supernatural beings did not exist. Though Wittgenstein seems to have had some sort of fundamental mystical religious beliefs, whereas Xunzi was more of a naturalist.

The whale shark genome reveals how genomic and physiological properties scale with body size. Dim on comparative genomics. But I do like sharks.

Harvard and the Brigham call for more than 30 retractions of cardiac stem cell research. The medical science literature is going to yield a lot of problems sooner than later.

Estimation of allele-specific fitness effects across human protein-coding sequences and implications for disease.

The Democrats Have a Latino Problem Hispanic voters were supposed to be the party’s future. It’s not working out that way.

Jason Collin’s on global fertility projections.

Bayesian Estimation of Species Divergence Times Using Correlated Quantitative Characters.

Hidden ‘risk’ in polygenic scores: clinical use today could exacerbate health disparities.

Identity inference of genomic data using long-range familial searches. If they solve the Zodiac killer, forget about the worries.

Inferring Demography and Selection in Organisms Characterized by Skewed Offspring Distributions.

Adaptive walks on high-dimensional fitness landscapes and seascapes with distance-dependent statistics.

Existence and implications of population variance structure.

Megalakes in the Sahara? A Review.

On this week’s episode of The Insight we’re talking about the genetics of the Uralic peoples, and Finns in particular.

Have you been noticing more intrusive and stranger advertisements in the media? That’s because it’s in trouble. The whole sector. But you knew that.

Nikki Haley shows she’s a good politician in regards to religion too

Filed under: Nikki Haley,Politics — Razib Khan @ 12:29 am

This week on The Remnant podcast, Jonah Goldberg, whose wife works for Nikki Haley, expounded at length about her skill as a politician. His point, which is legitimate, is that Haley is well liked by the broad mass of Trump-supporting Republicans (if not elite pro-Trump idealogues), as well as Trump-skeptical conservatives.

I’ve known of Nikki Haley since 2004, a few years after Bobby Jindal came onto to the national scene. Both are conservative Indian American Republicans elected as governors in the South. But there are differences between the two. While Haley can arguably “pass” as white, Jindal cannot (both are of Punjabi ethnicity). But a bigger difference has been their attitude toward religion: Jindal has worn his Christian conversion and faith on his sleeve, while Haley has been much more low-key. Throughout her career, Haley has admitted that the Sikh gurdwara remains a part of her life, despite her conversion to Methodist Christianity. Could you imagine Jindal saying such a thing about a Hindu temple?

The above is a video clip of Haley during a 2014 visit to India, where she visited the Golden Temple with her husband. When asked about her conversion to Christianity, she avers the sincerity of her belief. But Haley also speaks in an ecumenical language and seems to express the view that her choice of religion was in keeping with her culture as an American. Her turn to Christianity was not a denial of Sikhism, which she seems to see as grounded in India.

I can’t look into Haley’s heart, and to be frank her religious faith is not my business. But, I think I can say many people of subcontinental background tend to view converts to American Christianity as opportunists or somehow lacking in cultural pride and internal strength. American evangelical Protestant acquaintances would often mock Hinduism in front of me, despite the fact that I have a Muslim name and have been an atheist since I was a small child. To convert to Christianity is perceived by some to be conceding the point of that mockery.

And yet above Haley seems to be interpreting her conversion to Christianity as an expression of her alignment with the Dharma of the land in which she grew up, the United States. You may agree or disagree with her, but her emotional expression above certainly does make it seem that she retains a deep fondness for her Sikh upbringing.

October 13, 2018

Brown Pundits podcast, the Browncast episode 1

Filed under: Podcast — Razib Khan @ 11:02 pm

I’ve already submitted to iTunes and Stitcher. So I’ll post those links for those of you who want to subscribe that way….

The leisure class of the ancient world

Filed under: History,trade — Razib Khan @ 8:06 pm

The years before 1914 and the First World War are often termed the “first age of globalization” (with our current era the second). But that’s a little short-right, even though arguably correct in some sense.

Books such as The Fate of Rome and The Fall of Rome: And the End of Civilization make it quite clear that Classical Antiquity achieved some level of globalization in its corner of Eurasia. At the other end of Eurasia, the Grand Canal also illustrates the importance of trade and economic interdependence in complex pre-modern societies.

But what has been made can be unmade. One of the major arguments in Framing the Early Middle Ages is that the decline in the social complexity of the early medieval period in Europe was due in part to the collapse of the whole fiscal apparatus of the Roman bureaucratic state. Some of these weak post-Roman states were really chiefdoms bound together with personalized rule. A process which advanced the furthest in Britain and the Balkans.

And yet during the first grat maximum of human civilization in the years after 0 international trade extended even beyond the bounds of specific imperium, from one end of Eurasia to the other.

The Roman Empire and the Indian Ocean: The Ancient World Economy and the Kingdoms of Africa, Arabia and India focus mostly on the international aspect of the trade. Much of it is concerned with the role of conspicuous consumption among elites in the Roman Empire in driving this trade, and so the bullion drain to the east. Silk, incense, ivory, and medicines were all imported in large quantities from the east. The state benefited in some sense through taxation, but the drain on specie was a constant consideration. It is well known that Roman coinage, sometimes modified, became the standard in the southern half of India in the first centuries AD.

In a stepwise fashion, East Roman traders pushed across the Indian ocean until in 166 we know that they reached the imperial court in China. This connection seems to have been made by following the trade routes which were already established by Indians into Southeast Asia. Roman geographers were familiar with the general shape of Peninsular Malaysia, as well as Java.

Because our records from China and the Roman Empire are very good, is easy to ignore the reality that a whole network of cities existed along the shores of the Indian ocean. These cities grew up around trade and acted as intermediaries for the demand for particular luxury goods which also pumped specie out of Roman mines. But the decades after the Antonine plague seems to have been defined by multiple regressions across Eurasia, as societies dependent and expecting trade faltered when local nodes collapsed and interrupted the flow.

October 12, 2018

A historical slice of evolutionary genetics

Filed under: Evolutionary Genetics — Razib Khan @ 1:10 am

A few friends pointed out that I likely garbled my attribution of who were the guiding forces between the “classical” and “balance” in the post below (Muller & Dobzhansky as opposed to Fisher & Wright as I said). I’ll probably do some reading and update the post shortly…but it did make me reflect that in the hurry to keep up on the current literature it is easy to lose historical perspective and muddle what one had learned.

Of course on some level science is not as dependent on history as many other disciplines. The history is “baked-into-the-cake.” This is clear when you read The Origin of Species. But if you are interested in a historical and sociological perspective on science, with a heavy dose of narrative biography, I highly recommend Ullica Segerstrale’s Defenders of the Truth: The Battle for Science in the Sociobiology Debate and Beyond and Nature’s Oracle: The Life and Work of W.D. Hamilton.

Defenders of the Truth in particular paints a broad and vivid picture of a period in the 1960s and later into the 1970s when evolutionary thinkers began to grapple with ideas such as inclusive fitness. E. O. Wilson’s Sociobiology famously triggered a counter-reaction by some intellectuals (Wilson was also physically assaulted in the 1978 AAAS meeting). Characters such as Noam Chomsky make cameo appearances.

Segerstrale’s Nature’s Oracle focuses particularly on the life and times of W. D. Hamilton, though if you want that at high speed and max density, read Narrow Roads of Gene Land, Volume 2. Because Hamilton died before the editing phase, the biographical text is relatively unexpurgated. Hamilton also makes an appearance in The Price of Altruism: George Price and the Search for the Origins of Kindness.

The death of L. L. Cavalli-Sforza reminds us that the last of the students of the first generation of population geneticists are now passing on. With that, a great of history is going to be inaccessible. The same is not yet true of the acolytes of W. D. Hamilton, John Maynard Smith, or Robert Trivers.

October 11, 2018

Why PCA and genetics are a match made in heaven

Filed under: Evolution,Genetics,science — Razib Khan @ 8:13 pm
Insitome customers and selected populations

The image above is not the work of a small child trying to sketch out a B-2 Stealth Bomber. Rather, it is a PCA plot, which shows the distribution of a subset of Insitome’s customers who have purchased the Regional Ancestry Insight — in terms of how they relate to each other genetically.

In green, I have added some British individuals, in red some Africans from Nigeria, and in blue individuals who are ethnically Chinese. The majority of our customers are of Northern European heritage, but a substantial minority are African-American or Asian-American and various mixes therein.

So why do we use Principal Components Analyses, PCA, in the first place? And how does it work to matches our intuitions about relatedness through abstruse mathematical formulae?

Why we use PCA in genetics

Real genetic varition…a little bit

Consider this slice of diversity to the left. Six individuals, top to bottom, genotyped on a small number of genetic positions, left to right. You should recognize the letters, as they are DNA base pairs, A, C, G, and T. You can see above that there are variations between the positions across individuals. Now imagine attempting to gain insight from looking at thousands of individuals (rows) across hundreds of thousands of markers (columns).

Raw genetic data is basically just a huge text file. When you are concerned with the variation on a single position, you can view from the results for individuals or populations in a table and expect most people to immediately understand the implications. Europeans who are lactose tolerant have a variant on a particular marker. If you are TT or CT you can digest milk sugar, lactose, as an adult. If you are CC, you can’t. There are only one a few things to keep track of: the person, and their genotype.

Representing variation on a single marker, a single variable, isn’t necessary because the human mind can process all that information. In contrast, lots of simultaneous variables are impossible to understand just by visually looking at a table. PCA is just one of many excellent ways to extracting signal out of the noise.

The plot to the left was generated from ~30,000 markers on a few hundred individuals from eight populations. This is not a large dataset today. The time it took to run the function which generated the raw PCA result output was the period between me pressing “enter” on the keyboard and me looking at the computer screen.

And yet despite the modesty of this dataset can you imagine me looking at 30,000 variables across 200 samples, and obtaining any understanding? Perhaps if I devoted my life to the project!

What about the math?

The way it works mathematically is that it takes the voluminous raw data, which is totally incomprehensible to the human mind and summarizes it into a set of independent equations — making it completely essential to the analytical toolkit. The data is actually a “matrix.” PCA transforms it with a series of distinct equations which can define the total variation of the underlying data.

A matrix of genotypes

These equations, or more properly dimensions, are arrayed in order of proportion of variation in the data explained. On a conventional PCA plot, you see the first two dimensions, which explain the largest and second largest proportion of the variation, as the x and y-axes. But there are many more dimensions you can break the data apart by, though quite often for genetic analysis the largest ones are sufficient to smoke out the population structure that you are interested in. The values of individuals in each dimension that drops out of the data can then be placed onto a coordinate system, which is much easier to digest than a table of raw variation.

The branching of human populations

But how can a mathematical framework make biological variation comprehensible through maps so well — especially with regards to genetic differences between populations? The answer to this is straightforward: human evolutionary history has a pattern, and that pattern leaves its stamp on the genome. PCA is just a pattern extraction method.

The raw material of variation are mutations, and the pattern of mutations in any human genome is defined by a pedigree back to common ancestors. People who tend to share common ancestors share mutations — and mutations are the raw material for the genetic variation that PCA summarizes.

When used in evolutionary genetics, PCA should ideally recapitulate the phylogenetic tree. Assuming that sample sizes are balanced, humans in worldwide datasets have the first principal component of variation, which invariably a dimension that separates Africans from non-Africans.

Why? Because this is the earliest separation between large lineages, and so this ‘separation’ has had the most time to accumulate distinct and unique mutations in their two respective lineages. The second dimension is usually one that defines the difference between people from the Eastern portion of Eurasia and those from the western portion of Eurasia. Again, this is an important phylogenetic distinction because these two groups seem to have diverged soon after their ancestors left Africa.

And so on. PCA is not the only way to visualize the data. If you run a computer program that counted up raw similarities and differences between individuals at each genetic position, you would notice that some individuals are more similar to others, some groups more similar to other groups, and this too would reflect the phylogenetic history. If you had more time and wanted to dig deeper, you could construct various models of population history, and see how well the data fit those models.

PCA is not the only way to understand genetic variation. PCA itself is not the genetic variation, but a way to represent that variation, but it is a fast method that starts with few assumptions and lends itself to easy graphical representation. It’s not coincidence that it remains popular to this day.

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

Why PCA and genetics are a match made in heaven was originally published in Insitome on Medium, where people are continuing the conversation by highlighting and responding to this story.

Making what Harvard is about transparent

Filed under: GSS,Harvard — Razib Khan @ 8:03 pm
This is the future Edward Blum wants

In the 20th century version of the TV series Murphy Brown, there was an episode where three young American scholars were introduced. The big laugh was that they had very Chinese or Indian names. Though it’s probably politically incorrect today to depict it that way, the joke is that the best “American” scholars were not really American….

If you’re an Asian American who remembers the period before the 1990s, you know where I’m coming from. This was an America in black and white, and you were literally the Other if you were outside of those two boxes. People would be surprised that you spoke English without an accent, and inquire where you really came from. This still happens now and then, but back in the 1980s, it was pervasive. It was tradition. The children of the first post-1965 immigrants were not yet grown, so the majority of Asian American adults you saw and encountered were immigrants outside of a few areas, such as Hawaii and portions of the West Coast. In 1980 1.7% of the people residing in the United States were Asian American. Today nearly 7% are Asian American.

This is having an impact. The winners of spelling bees and science fair winners don’t “look like America” anymore.

And this is the major reason why the cultural elite is very upset about the scrutiny which admissions processes at top universities have been receiving. Consider this op-ed in The New York Times, A Damaging Bid to Censor Applications at Harvard. It concludes:

As a leader in higher education, Harvard is trying to change this through its modest consideration of race in admissions. Its goal is to create a diverse community of students who can engage with and learn from people who are different, and carry those experiences with them beyond the university.

Expressions of racial identity are part of the fullness of our humanity. It’s not possible to be blind to race. Pretending as though it is ensures we will forever be divided.

The op-ed is pretty measured and not particularly shoddy as far as it goes. This is the sort of message that the editors and reporters at The New York Times want to amplify. Call it the anti-Bari Weiss effect.

The problem I have with Harvard and its academic and administrative overclass is that the media often allows them to engage in doublespeak without any comment, critique or dissent. Part of it is that institutions such as The New York Times are dominated by people from elite academic institutions, and so are part of the same broad culture, with a set of assumptions and interests, implicit and explicit, private and public. They’re all family.

For example, a few years ago the president of Harvard declared that the institution was all about inclusion. On the face of it that is just a bald-faced lie, and everyone knows it. Harvard is about exclusion, selection, and curation. “Inclusion” actually meant that there are certain views and backgrounds that Harvard is going to curate and encourage. Which is fine. But an institution which excludes >95% of those who apply for admission is by definition not inclusive and open.

The issue with Harvard is that it is an institution which is many things to many people. Harvard lets in the smart, talented, wealthy, and powerful, with various mixes of these elements. Asian Americans tend to be smart and talented in academic measures, but most of them are not “old money” in the United States, and even if they were there is a suspicion (perhaps fair, I don’t know) among many stewards of elite academic institutions that they don’t have the values which would result in large donations to those institutions. Harvard needs to take care of rich people, who tend to be white, and lucky, because it wants rich people to take care of Harvard. Luckily for the rich, they are not always so smart and diligent, but they are “well-rounded.” Their personalities have polish, and if that’s not there, perhaps a strategic donation can be made.

Harvard also smiles upon the scions of Third World dynasties. They may not be brilliant, but they are likely to impact the lives of hundreds of millions through their possible ascension to the pinnacle of power. Again, in clear doublespeak, Harvard mouths egalitarianism constantly but signals in its actions that it is realistic that power is passed down through blood. Harvard is in and of this world. It makes the world. And the world makes it.

Finally, Harvard educates the American ruling class. And it wants to continue to educate the American ruling class. As such, it is self-conscious of the fact that it, therefore, can’t have the demographic profile of Cal-Tech. Harvard doesn’t just want to incubate innovators, it wants to cultivate and train the administrators of the largesse that innovation allows.

The “diverse community of students” who are going to become elected officials is no doubt one reason that Harvard and other elite schools make recourse to racial and regional diversity metrics. If Harvard can be thought of as a finishing school for the elites attached to a hedge fund (its endowment), it needs to maintain some diversity in its portfolio of the future overclass. Legacies and the super-rich are important because these are lineages with a record of success within the overclass. The data is clear that innate cognitive aptitudes aside, children of privilege have a leg up. All things equal, and even not equal, it is rational to give bonus points to those who come from privilege if you want to maintain your own as an institution.

But, you also need to sample more of the parameter space. Some families do leave the elite, and others join it. The goal of an institution like Harvard is to admit and cultivate potential joiners. These are not always going to be children who win spelling bees and science fairs, and can attain every metric you might put in front of them. Political leaders of given communities tend to look like and come from those communities. Therefore, there is a need to maintain some level of racial and ethnic diversity if power, as opposed to academics,* is your number one focus.

What if Harvard began to let more Asian Americans in? Even though it is a private institution it would have some of the problems that Stuyvesant High School in New York is facing. Stuy is about 75% Asian American in a city that is 12% Asian American. The plain fact is that an elite public school supported by the city is probably not sustainable in the long-term if it does not reflect the demographics of the city. This is not an argument about whether it is just or not, but an observation of the dynamics of power and influence in a democratic system.

Harvard has to look somewhat like America visibly. The visibility part is important because it makes it salient. The reality is that Harvard undergraduates are highly atypical in their family background. The average student comes from a family in the top 20% of household income distribution. This distribution is probably multi-modal because Harvard’s endowment allows it to subsidize students of more modest means while still reserving spots for the extremely wealthy and privileged. Additionally, when you scratch beneath the surface the “visibility” can deceive. Harvard representation of black students is near the national proportion. But historically the majority of these have been from biracial or immigrant or Caribbean American households. In the 2000s it was estimated that one-third of Harvard black students represented 90% of black Americans who have four grandparents who were born and raised in the United States as black Americans.

But from what I can tell the issue of at last superficial visible identity is key, and substantive differences which are not externally salient less critical. The fact that the first black American president had a white mother and an African immigrant father has been noted, but over time it seems to be less and less important than the fact that he identified and was seen as a black American, despite his atypicality on so many substantive measures.

The problem though is that even though visibility matters, unanimity of viewpoint and opinion may cause problems in pumping the pipeline to power in a democratic republic where there is still a pluralism of views. Harvard undergraduates are very liberal and secular compared to the American public. Not that there’s anything wrong with that. But if you want to be the training ground for power, in a democratic republic where there are still differing views it is important that one expect those views and anticipate responses (though clearly a lot of politicians lie about their piety and ‘evolve’ in their ideology).

In particular, Christian white conservatives are far less well represented at Harvard than they are on a national level. Obviously, there is not anything wrong with that as such, but historically we’ve had white Christian conservatives (or people who identify and affiliate as such) in positions of power, and their exclusion from elite institutions might engender alienation and hostility from the very power that they exist to cultivate.

Of course, it could just be that white conservative Christians are not academically up to snuff. My previous inquiries do suggest there is a strong correlation between secularity and social liberalism and very high IQs. But, if you look at the GSS’s WORDSUM variable you see there are probably a reasonable number of intelligent white conservative Christians.

First, looking at the WORDSUM scores of non-Hispanic whites by ideology, you can see that liberals tend to be smarter than conservatives, and both are smarter than moderates. This is a pretty robust pattern. Intelligent people tend to have stronger and more strident views. Moderates are probably moderate in part because they aren’t as bright and so have weak opinions.

That being said, when you look at the distribution of ideologies by WORDSUM scores you get a different perspective. Though moderates are on average less intelligent, there are so many of them that for non-Hispanic whites they are still the most numerous in the 9-10 category (that is, they got one item wrong, or none wrong). And, there is balance between the number of conservatives and liberals. The average liberal is smarter, but the much larger number of white conservatives means that even in the brightest decile they attain parity.

Of course, the average Harvard student is not a top 10% performer, they’re a top 1% performer. And often not just academically, but in a variety of ways. They are selected for raw intelligence, but also high conscientiousness. Though the two are correlated, they are imperfectly so. Following James F. Crow’s expectation in regards to human inequality, when you select from the intersecting tails of multiple different distributions, the resulting student population is unlikely to be representative of the broader population.

Let’s wrap this up with some conclusions.

First, Harvard and the other Ivies will find a way to continue to cap the number Asian American students. I think the current lawsuit may win on the merits, but the “Deep Oligarchy” is more powerful than the judiciary or the executive branch. If, on the other hand, Harvard gets rid of legacies and special backdoor admissions, I’ll admit I was wrong, and the chosen have lost control of the system. As long as legacies and backdoor admissions continue, you know that the eyes are on the prize of power and glory. Capping the number of Asian American “grinds” would be a small price to pay then, and those who are allowed beyond the gates will be well-trained to sing the praises of Harvard’s policy (as they all do).

Second, the alienation of the successor to the “Eastern Establishment” from the large numbers of moderate and conservative whites will be a long-term problem in terms of the maintenance of its grip on power. Though this segment of the population is in decline, it is still large and substantial, and will wield power and influence out of proportion to its overall numbers for decades because they are older. They vote more, and they mobilize well. The rise to dominance of ideologies at campuses such as Harvard which pathologize the very persistence of these groups on the national scene will exacerbate the polarization and alienation. Though the individuals who run these institutions may bemoan this trend, because of the large numbers of students who are ideologically on the same page on this issue, they won’t be able to stop the march toward cultural radicalization.

Harvard has avoided the problem of Stuyvesant by maintaining visible diversity within its student body. But because it does not emphasize intra-racial ideological diversity, it will eventually run into its own Stuyvesant problem as it loses all legitimacy from large swaths of the body politic who see that racial identity does not entail ideological affinity and sympathy.

Addendum: This is a mildly obscure blog. And to be honest I’d rather write about science papers than this. But, I wanted to put this blog post up so that it’s out there, because mainstream publications seem to be intent on publishing a stream of what I perceive to be simplistic or disingenuous pieces.

The Left/liberal/progressive side engages in cant about “diversity”, when we all know they mean a very precise sort of diversity, and a very particular type of background when they talk about “background.” But the Right/conservative side’s emphasis on merit and colorblindness strikes me as consciously blind to the fact that these institutions were always about shaping and grooming the elite, and engaged in the game of reflecting and determining the American upper class. The Right/conservative project would abolish Harvard as we know it on a far deeper level than the Left/liberal/progressive posturing cultural radicalism, which at the end of the day has no problem bowing before neoliberal capital so long as lexical modifications are made.

If Asian Americans want to increasing their proportion at Harvard, they have to follow the Jewish strategy and join the socio-political elite. If they don’t do that, then the Asian quota will persist in some way.

* When I speak of students and “Harvard” I’m talking about the undergraduate level. The graduate and professional schools are somewhat different.

October 10, 2018

An “in-fill” framework for the expansion of peoples in Europe: beakers, beakers everywhere!

Filed under: Ancient DNA,Beaker people — Razib Khan @ 10:04 pm

In the 1970s A. J. Ammerman and L. L. Cavalli-Sforza argued for the validity of a model of Neolithic expansion of farmers into Europe predicated on a “demic diffusion” dynamic. This is in contrast to the idea that farming spread through the diffusion of ideas, not people. The formal theory is inspired by the Fisher wave model, but empirically just imagine two populations with very different carrying capacities due to their mode of production, farmers, and hunter-gatherers. In a Malthusian framework, the farmer carrying capacity in a given area of land might be ~10× greater than that of hunter-gatherers. Starting at the same initial population, the farmers will simply breed the hunter-gatherers out of existence.

As the farmers reaching their local carrying capacity, migration outward will occur in a continuous and diffusive process. For all practical purposes, the farmers will perceive the landscape occupied by hunter-gatherers as “empty.” This is due to the fact that hunter-gatherers often engage in extensive, not intensive, exploitation of resources. In contrast, even slash and burn agriculturalists leave a much bigger ecological footprint. They swarm over the land.

The beauty of the demic diffusion process is that that it’s analytically elegant and tractable. Families or villages engaged in primary production to “fill up” a landscape through simple cultural practices which manifest on the individual scale that allow for aggregate endogenous growth. And this model underlies much of the work by Peter Bellwood in First Farmers and Colin Renfrew’s theories about the spread of Indo-European langauges. You can call it the Walder Frey theory of history.

I didn’t really think deeply about this theory because I didn’t have much empirical knowledge until I read Lawrence Keeley’s War Before Civilization. In this book, Keeley observes that the archaeological record suggests that there was violent conflict between the first farmers and hunter-gatherers in northwestern Europe, near the North Sea. He reports that there seems to have been a broad front of conflict, presumably a prehistoric “no man’s land.” Not only that, but Keeley claims that the spread of agriculture stopped for a period. The barrier between hunter-gatherer occupation and farmer territory was not permeable. Not diffusion.

As a stylized fact, the demic diffusion framework treats all farmers as interchangeable and all hunter-gatherers as interchangeable. On the face of it, we know that this is wrong. But the assumption is that to a first approximation this axiom will allow us to capture the main features of the dynamics in question. This may be a false assumption. The fact is we know that some hunting and gathering populations can engage in intensive resource extraction and remain sedentary.

Intensive hunter-gatherers

The Pacific Northwest Indian tribes of the United States of America are the best-known examples of such hunting and gathering peoples. Because of the concentrated runs of salmon, these people could remain hunter-gatherers while maintaining relatively sedentary and dense societies characterized by social stratification (e.g., they practiced slavery). As it happens, it seems that it is on the maritime fringes of Northern Europe than the hunter-gatherers flourished the longest. Agriculture took ~1,000 years to transplant itself from northern Germany to southern Scandinavia, and even then hunter-gatherer lifestyles persisted in many locales for several thousand years until the Nordic Bronze Age (and in Finland even longer).

The flip side of the variation in intensity and density of hunter-gatherers is that the early farmers were probably less efficient and intensive than later agriculturalists. And, as the Anatolian farmers pushed into Northern Europe their cultural toolkit would be less and less effective. Even assuming local dynamics of reproductive increase as the primary driver for farmer expansion, the growth parameter of the agriculturalists in comparison to the hunter-gatherers may not have been that different in many contexts.

But the second major issue is that the assumption of continuous and diffusive expansion over wide areas is probably wrong. The early Neolithic farmers may have been stateless in a modern sense, but they were almost certainly not primitive anarchies. They were pre-state polities of some sort no doubt and exhibited coordination and cultural uniformity over large distances. An illustration of what might happen to small groups of farmers is what happened to white American homesteaders who occupied territory too close to the Comanche lands. Future archaeologists may see an empirical pattern of demic diffusion of white Americans from the east to the west, but that expansion occurred only within the scaffold of a political-military superstructure.

On a fundamental level demic diffusion, and the higher reproductive value over time of farmer peoples than hunter-gatherer peoples, are essential pieces of the puzzle of the peopling of Europe during the Holocene. But they need to be framed in the context of the discontinuous expansion of cultural zones of activity and freedom for farming communities, under the umbrella of some supra-village social and political order. This step by step expansion in a piecewise fashion probably explains the “hunter-gatherer resurgence” that David Reich’s lab has found in the temporal transects within a given region. Even if socially and politically dominant within a particular region, the farming communities likely targeted the richest and most suitable lands as predicted by classical economics. The hunter-gatherer populations likely persisted in more marginal areas and only assimilated with the dominant farmers over time. The invasion dynamics locally would exhibit patchiness in the early phases, allowing for hunter-gatherer persistence.

The fundamental lower-level dynamics are those of panmictic local populations expanding over time in a continuous fashion. These can be modeled by a few parameters. The problem is that the older idea that this could be generalized over time and space is surely wrong. Rather, inter-group dynamics probably govern a lot of the coarse-scale patterns we see. Over time farmer populations always won, but “on any given day” the outcome was always in doubt.

And so it was with agriculturalist conflicts as well. This is on my mind partly because I recently reread Genetic origins of the Minoans and Mycenaeans and The Beaker Phenomenon and the Genomic Transformation of Northwest Europe. There are lots of details within these papers that are easy to miss on first or second or even third read. For example, I noticed a sample dated to between 2200 and 1900 BC (so probably 2050 BC?) from Parma in northern Italy from a Bell Beaker cultural context which has a lot of steppe ancestry. Contemporaneous samples from Iberia seem spottier in their steppe ancestry, but that’s around when it shows up in that peninsula. Similarly, steppe ancestry arrived in Greece at some time after the Neolithic but before the Bronze Age collapse.

We know that the Beaker people arrived in Britain and Ireland rather suddenly ~2500 BC, even though the earliest evidence of the canonical beakers diagnostic for this culture are found in western Iberia in ~2900 BC. The Reich group concluded, rightly I suspect, that the cultural phenomenon of the Beaker people transcended a particular socio-cultural group bounded by kinship and genetic affinity. In other words, the Beaker culture was a set of peoples, in the plural.

And yet outside of Iberia and some Mediterranean locales, The Beaker Phenomenon and the Genomic Transformation of Northwest Europe makes it clear that a genetic disruption of the local demographics occurred when the society adopted the beaker. Whereas in Central and Eastern Europe Indo-European languages probably arrived with the Corded Ware people ~2900 BC, the Beaker come to our attention somewhat later, and in fact, pushed eastward into Corded Ware territory. Though the Beaker people seem to have been the vectors for steppe ancestry in many areas of Western Europe, they generally have less of it than the Corded Ware.

The Corded Ware frontier with non-Indo-European peoples to their west, south, and north, can be thought of as a cultural innovation zone. This is historically the trend, with frontier areas producing a vigorous and cohesive, yet often innovative, identity group that can mobilize resources and engages in expansion and domination. The Zhou and Chin states in China are examples of this, as is the ascendence of Roman Emperors from the trans-Danbunian region after 200 AD. It seems entirely possible then that the explosion of Indo-European Beaker people on the West-Central European frontier occurred through cultural synthesis and transmission from non-Indo-European Western Europe of the 3rd millennium, and once this society became cohesive it expanded outward aggressively.

In sum, while genetic processes are continuous and gradual, cultural processes are often discontinuous and may exhibit a phase of fluctuating change alternating stasis (perhaps modeled by a Poisson distribution of periods of expansion against the typical stationary background state?).

Addendum: The Slavic expansion in Eastern Europe and the Balkans fits with this model. Their success both demographically and culturally was due in large part to an ability to adapt to the regression of social complexity. Slavic societies were antifragile. They degraded well. In contrast, the Latin and Greek peasantry were more reliant for their existence and cultural continuity on the Roman state. With the collapse of the Balkan limes in the last quarter of the 6th century, the East Roman Empire lost total control of its Europeans interior communications, and Constantinople, Thessaloniki and the Peloponnese remained connected through maritime means through the Imperial navy’s total control of the Aegean.

And the Slavs were not an anarchic people. Though organized around small tribes, they existed under the hegemony of the Avars, and in multiple instances seem to have coalesced under the leadership of non-Slavic peoples who provided a leadership caste before these groups were culturally assimilated. Their demic diffusion through the Balkans was only enabled through the scaffold of an expansion pastoralist ascendancy in areas heretofore dominated by the Roman state.

October 9, 2018

Reflections on the biology of Homo calaquendi

Filed under: Elves,Fantasy,Tolkien — Razib Khan @ 7:37 pm

For a while now I’ve been really haunted by a question about the verisimilitude of J. R. R. Tolkien’s world-building: what are the long-term social and biological consequences of the fact that the Eldar, the elves, are immortal?

Consider the fact that the elves are long-lived, and not particularly fecund. Even when they are, inter-general patterns are spotty. Fëanor had seven sons, but only one grandson! Today we have “helicopter parents”, always worried about the safety of their offspring. How would an elvish society ever flourish if parents are terrified about the risk of their few offspring dying prematurely?

The fact that elves even go to war is indicative of a very strange and alien psychology. If you had the opportunity for everlasting life, would you risk it in battle? Are elves courageous? Or do they just have high time-preference?

But for me, the bigger question is the psychology of Galadriel. At 7,000 years old she is one of the oldest creatures in Middle Earth, along with Gandalf, Sauron, Cirdan, and Glorfindel. Assuming 100 years that’s 70 human lifetimes. J. R. R. Tolkien is quite clear about her physical appearance. She is quite tall, with silver-gold hair. But her head is not particularly large. So the question presents itself: how does her long-term memory allocation work? We know she has a human cranial capacity.

If salient and emotionally resonant memories connected to excitement in the hippocampus are the ones banked, does that mean that Galadriel’s mind is brimming with incredibly vivid recollections? Shouldn’t she be depressed in the present, because the present is going to be so dull compared to her glittering memories of Aman, and the beauty and elegance of the First Age civilization of the Eldar?

Additionally, it seems clear that the Eldar don’t suffer from cognitive decline in the same way as humans. Does that mean perhaps that Galadriel’s intuitive abilities would be suprahuman? Both humans and elves are children of Eru Ilúvatar. There is no evidence from the legendarium that elves are orders of magnitude more gifted than humans in “system 2” thinking, that is, rational reflection. But in their grace and acuity in matters of perception are curious. Could be it be a function of acquired “system 1” faculties, as opposed to what they were born with?

Perhaps the fey grace of the Eldar is not a matter of their natural abilities, but a function of developmental psychology? If the 10,000-hour rule is a thing, how about the 100-generation rule?

Finally, the elvish recourse to writing strikes me as peculiar in light of their immortality. They seem to be primary producers and foragers who don’t engage in much trade, so accounting is not highly valued in all likelihood. And writing does not confer the gains of the advantage of immortality to an already immortal species.

Note: For those readers who suggest that this post may mean that I never have sex, I already have three children. That’s more than most elves!

The post-neutral human genome (the Kern-Hahn era)

Filed under: Neutral Theory,Population genetics — Razib Khan @ 6:50 pm

If you have any background in evolutionary biology you are probably aware of the controversy around the neutral theory of molecular evolution. Fundamentally a theoretical framework, and instrumentally a null hypothesis, it came to the foreground in the 1970s just as empirical molecular data in evolutionary was becoming a thing.

At the same time that Motoo Kimura and colleagues were developing the formal mathematical framework for the neutral theory, empirical evolutionary geneticists were leveraging molecular biology to more directly assay natural allelic variation. In 1966 Richard Lewontin and John Hubby presented results which suggested far more variation than they had been expecting. Lewontin argued in the early 1970s that their data and the neutral model actually was a natural extension of the “classical” model of expected polymorphism as outlined by R. A. Fisher, as opposed to the “balance school” of Sewall Wright. In short, Lewontin proposed that the extent of polymorphism was too great to explain in the context of the dynamics of the balance school (e.g., segregation load and its impact on fitness), where numerous selective forces maintained variation. The classical school emphasized both strong selective sweeps on favored alleles and strong constraint against most new mutations.

And yet one might expect low levels of polymorphism from the classical school. The way in which the neutral framework was a more natural extension of this model is that even if most inter-specific variation, most substitutions across species, are due to selectively neutral variants, most variants could nevertheless be deleterious and so constrained. Alleles which increase in frequency may have done so through positive selection, or, just random drift. Not balancing forces like diversifying selection and overdominance.

The general argument around neutral theory generated much acrimony and spilled out from the borders of population genetics and molecular evolution to evolutionary biology writ large. Stephen Jay Gould, Simon Conway Morris, and Richard Dawkins, were all under the shadow of neutral theory in their meta-scientific spats about adaptation and contingency.

That was then, this is now. I’ve already stated that sometimes people overplay how much genomics has transformed our understanding of evolutionary biology. But in the arguments around neutral theory, I do think it has had a salubrious impact on the tone and quality of the discourse. Neutral theory and the great controversies flowered and flourished in an age where there was some empirical data to support everyone’s position. But there was never enough data to resolve the debates.

From where I stand, I think we’re moving beyond that phase in our intellectual history. To be frank, some of the older researchers who came up in the trenches when Kimura and his bête noire John Gillespie were engaged a scientific dispute which went beyond conventional collegiality seem to retain the scars of that era. But younger scientists are more sanguine, whatever their current position might be because they anticipate that the data will ultimately adjudicate, because there is so much of it.

With that historical context, consider a new paper, Background selection and biased gene conversion affect more than 95% of the human genome and bias demographic inferences:

Disentangling the effect on genomic diversity of natural selection from that of demography is notoriously difficult, but necessary to properly reconstruct the history of species. Here, we use high-quality human genomic data to show that purifying selection at linked sites (i.e. background selection, BGS) and GC-biased gene conversion (gBGC) together affect as much as 95% of the variants of our genome. We find that the magnitude and relative importance of BGS and gBGC are largely determined by variation in recombination rate and base composition. Importantly, synonymous sites and non-transcribed regions are also affected, albeit to different degrees. Their use for demographic inference can lead to strong biases. However, by conditioning on genomic regions with recombination rates above 1.5 cM/Mb and mutation types (C↔G, A↔T), we identify a set of SNPs that is mostly unaffected by BGS or gBGC, and that avoids these biases in the reconstruction of human history.

This is not an entirely surprising result. Some researchers in human genetics have been arguing for the pervasiveness of background selection, selection against deleterious alleles which effects nearby regions, for nearly a decade. In contrast, there are others who argue selective sweeps driven by positive selection are important in determining variation. Unlike the 1970s and 1980s these researchers don’t evince much acrimony, in part because the data keeps coming, and ultimately they’ll probably converge on the same position. And, the results may differ by species or taxon.

If you want a less technical overview than the paper, Kelley Harris has an excellent comment accompanying it. If you want to know what I mean by the Kern-Han era, it’s a joke due to the publication of The Neutral Theory in Light of Natural Selection.

Finally, some of you might wonder about the implications for demographic inference which preoccupies me so much on this weblog. In the big picture, it probably won’t change a lot, but it will be important for the details. So this is a step forward. That being said, the possibility of variable mutation rates and recombination rates across time and between lineages are also probably quite important.

Open Thread – Brown Pundits

Filed under: Open Thread — Razib Khan @ 6:28 pm

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

How the Greeks came to be

Filed under: Greeks,History — Razib Khan @ 4:01 pm

Sing, Goddess, Achilles’ rage,
Black and murderous, that cost the Greeks
Incalculable pain, pitched countless souls
Of heroes into Hades’ dark,
And left their bodies to rot as feasts
For dogs and birds, as Zeus’ will was done.

Who are the Greeks? Where did they come from?

We have enough ancient DNA now to answer many of these questions. It seems that the largest component of Greek ancestry derives from the expansion of farmers out of Anatolia ~9,000 years ago. But at some point in the latter phases of prehistory, another wave of migrants pushed out from the east, with affinities to peoples as far away as Iran. And then during the Bronze Age, another pulse of migration arrived, likely correlated with the arrival of Greek-speaking peoples as such, the Mycenaeans. Finally, there is a fair amount of circumstantial evidence that the peregrinations of the pagan Slavs during Late Antiquity and the early Medieval period left their imprint on many Hellenes, in particular in the north of the country, around Salonika.

But that’s just genetics. What about culture? In terms of religion, Greek paganism is a composite. Zeus pater is clearly a standard Indo-European sky-god. Jupiter in Latin. Dyáuṣ Pitṛ́ for the ancient Aryans. In contrast, gods such as Athena seem to have synthetic, and at least partly pre-Indo-European origins. Finally, Dionysius was possibly an eastern import relatively late in prehistory.

Though the Greek language is definitely Indo-European, there are also extensive loanwords indicating an indigenous substrate. For example, words with the syllabic fragment nth, such as in Hyacinth, are likely native. The Greeks settled amongst peoples who had a long history of settled life, and had developed their own civilization.

The point is that it is probably not even wrong to say that the Greeks as we understand came from elsewhere, or, that they were indigenous. To be Greek probably emerged in the period after 2500 BC, as Indo-Europeans mixed with the local cultures, and created something new. Autochthonous.

October 8, 2018

Brown Pundits Browncast

Filed under: Podcast — Razib Khan @ 8:58 pm

So at some point the Brown Pundits “browncast” (as opposed to brown caste) is a go. I’m not going to submit to Itunes or Stitcher until we have a podcast recorded and up.

Open Thread, 10/8/2018

Filed under: Open Thread — Razib Khan @ 8:03 pm

Paul Romer won the Nobel. Not a big surprise. David Warsh’s Knowledge and the Wealth of Nations: A Story of Economic Discovery is pretty good. I recommend it. I would read it in concert with Hive Mind: How Your Nation’s IQ Matters So Much More Than Your Own and A Farewell to Alms: A Brief Economic History of the World (Warsh wrote a negative review of the second book and likely would not be a fan of the first).

Analyses of Neanderthal introgression suggest that Levantine and southern Arabian populations have a shared population history. Bigger Yemeni data set. Yemeni and Levantine populations seem quite similar….

As you may not know Google+ was finally given an explicit sunset schedule. Google tried twice to tackle Facebook but failed both times. But it turns out that Facebook may never have a successor. A centralized social-graph has weaknesses, and younger cohorts seem to be creating segmentation. Their parents are on Facebook, so they have a nominal Facebook account. But the real action is on other platforms.

Life on the Dirtiest Block in San Francisco. Having drinks with friends at the top of hotels and high rise condominium complexes makes you forget that far below the homeless have come out and taken over the night.

Why most narrative history is wrong. First, this seems to be more about ‘popular’ history today, and the mainstream of past history. One reason contemporary academic history is so boring for most people is that it resists grand narrative temptation.

With that being said, this is more of an indictment on modern journalism.

Quantifying how constraints limit the diversity of viable routes to adaptation.

A Simulation-Based Evaluation of Total-Evidence Dating Under the Fossilized Birth-Death Process.

Expanded Pre-Implantation Genomic Testing.

Fudged statistics on the Iraq War death toll are still circulating today. Do you remember this debate more than ten years ago? I do. The very assertion of these numbers distorted the discourse. This was just a prefiguring of the media landscape today. It’s mostly propaganda.

Phylogeny, ancestors and anagenesis in the hominin fossil record.

The genetic relationship between female reproductive traits and six psychiatric disorders.

In case my Twitter account gets deleted, remember you can subscribe to my RSS or follow my Facebook page.

October 6, 2018

The derived SNP that causes dry earwax was not found in all non-Africans

Filed under: earwax,Population genetics,rs17822931 — Razib Khan @ 11:26 am

A new paper on Chinese genomics using hundreds of thousands of low-coverage data from NIPT screenings is making some waves. I’ll probably talk about the paper at some point. But I want to highlight the frequency of rs17822931 in Han Chinese. It’s pretty incredible how high it is.

Because the derived variant SNP, which is correlated with dry flaky earwax when present in homozygote genotypes, is also associated with less body odor, it has been studied extensively by East Asian geneticists. Basically, individuals who are homozygote for the ancestral SNP, which is the norm in Europe, the Middle East, and Africa, tend to have more body odor, and in societies and contexts where this is offensive these people are subject to more ostracism in East Asia as they are a minority (some of the studies in Japan were motivated by conscripts who elicited complaints from their colleagues).

The relatively low frequency in Guangxi is to be expected. This province was Sinicized only recently. As in, the last 500 years. And it still retains a huge ethnic minority population, and many of the Han in the province likely have that ancestry. But the question still arises: why do the Han have such a high frequency of rs17822931?

Here’s a plot of frequencies:


But the ALFRED database has more details. Sardinians, Somalis, Ethiopian Jews, and Dani from the New Guinea highlands all have very low proportions or none of the derived variant. The Ethiopian Jews are about ~40% West Eurasian, due to Middle Eastern agriculturalist ancestry. Groups like the Masai also have Middle Eastern agriculturalist ancestry. I think the low frequencies of the derived variant in the Middle East are due to migration from eastern Eurasia in the relatively recent past. The frequencies of the derived variant in Europe probably came with the Ancestral North Eurasian ancestry of the steppe people. In South and Southeast Asia the frequencies are indicative of balancing selection, even if there is no such selection, while in the New World world the derived variant is at low, but appreciable frequencies.

As I mentioned in an earlier post, a 40,000 year old Siberian had the derived variant (heterozgote). I suspect the Basal Eurasians did not.

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