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

June 25, 2017

Over the long term civilization matters

Filed under: Culture — Razib Khan @ 9:09 pm

In Peter Turchin’s work modeling human historical dynamics he introduces the idea of a “meta-ethnic” identity. Quite often this is synonymous with a world religion. These identities emerged in the last few years as human polities scaled so large as to expand beyond tribal-national boundaries.

These sorts of dynamics are clear when we think about the Crusades, the defense against the Ottomans in the 17th century, or the Iberian “division” of the world between Castile and Portugal. Common ties of civilization and identity allow for ingroup cohesion, as well as heightening hostilities against outgroups.

Of course there many exceptions. When reading The Great Sea: A Human History of the Mediterranean I recall being struck by how southern Italian city-states like Amalfi opportunistically allied with Muslim pirates against other Christian powers. Similarly, during the Battle of Vienna Protestant Hungarians marched with the Ottomans against the broader Christian alliance which came to the aid of the Habsburgs.

These are two instances which show short term self-interest or necessity driving choices of group coalitions. Amalfi, like later Italian city-states, found it in their interest to do business with Muslims, even if it was to the detriment of their co-religionists. This did not mean they were no longer Christians. But in many instances they put that identity aside for their own gains. In the case of the Protestant Hungarians there’s was an alliance of necessity.

As recounted in Divided by the Faith the decades leading up to the Battle of Vienna the Hungarians experienced a concerted campaign of conversion and persecution of the part of the Habsburg monarchy in concert withe Roman Catholic Church. The Habsburg’s Austrian lands were brought back fully into Catholicism, as was most of Imperial Hungary. It is no coincidence that Hungarian Reformed Protestantism was strong in the east, which had been under Ottoman influence. The arrival of an expansive Austrian monarchy was an existential threat for them.

The flip side are cases where groups with the same civilizational identity engage in wars over resources or boundaries. The conflict between Ethiopia and Eritrea would certainly fit into this mold, and to some extent the Great War in the Congo which has flared for two decades now.

This sort of dynamic has been used to argue that Samuel P. Huntington’s The Clash of Civilizations and the Remaking of World Order is not a useful framework. But on the contrary what Turchin and colleagues have shown is that over the long run civilizational fissures tend to result in the most vicious and dehumanizing wars.

Open Thread, 6/25/2017

Filed under: Open Thread — Razib Khan @ 8:53 am

I’m beyond the “keto flu.” That was tough.

A few months ago I asked a Hindu nationalist friend of mine the best persons who promote the “Out of India Theory.” One name he forwarded to me was Koenraad Elst. Though Elst and I disagree on facts in relation to the issue at hand, a reader has pointed out that he’s taken a very strident and clear stand against the ad hominem attacks against me from those who would consider him a fellow traveler. This honorable stance frankly has shocked me to my core, as I’m just not used to it after engaging with SJWs and various ideologues for so long. The ad hominem is so easy that it takes some fiber and integrity to resist it.

One consequence of Elst’s clear stand is that I think I do need to revisit some of his work.

Read some of The Enigma of Reason yesterday. I would recommend it. I’ve read some of Dan Sperber’s previous stuff, like Explaining Culture: A Naturalistic Approach, and it’s familiar. Also, Sperber was a major influence on Scott Atran, so even though this book is new many of its ideas and orientation are prefigured in In Gods We Trust.

SMBE 2017 in about a week at the JW Marriott in Austin. I’m not going to be there the whole time, but when I’m there I’ll be tweeting.

Waking Up With Sam Harris #83 – The Politics of Emergency (with Fareed Zakaria). I agree with Fareed Zakaria more on Islam.

A left-wing journalist is attacking Richard Dawkins on the basis of his family having had African servants when they lived in Kenya. This person is some sort of Max Blumenthal clone from what I can see. A fringe element of far Left basically has a modus operandi: pick someone to destroy, and extract elements of their life to flog them as evil (call them racist, sexist, something -ist).

This is great on Twitter, but not optimal for movement building. I understand that there is a reasonable, moderate, liberal, Left. But this radical Left wants many of us out there on the street, our families dispossessed. When the lines are drawn, this is why some of us will keep voting Republican despite all our issues with the party: we don’t want to be personally destroyed.

Related to the chilling impact of this behavior, Liberals and Immigration, Kevin Drum says:

I have no idea what, if anything, we can do about this. But I will say this. I lurk on a number of message boards populated by liberals, and what they say privately is very often more nuanced than what they say publicly.¹ On immigration, there are probably lots of liberals willing to concede that there needs to be a limit to the flow of undocumented workers. There are cultural, economic, and nationalistic reasons for this. But there’s little benefit to saying so in public. It just invites massive, social media swarms insisting that you’re a closet racist.

White Cheese is white Supremacy

This is in response to Peter Beinart’s piece How the Democrats Lost Their Way on Immigration. I think Michael Brendan Dougherty has a pretty good response to this in National Review. Before he wrote this piece he observed on Twitter that Beinart wasn’t confronting something that had changed on the Left. I responded: “white supremacy.”

White supremacy has gone from being the KKK or Neo-Nazis, to basically all of American society. The term is used liberally and without much care. Just like the term racist or sexist. It’s both a cudgel in tactical debates, and, for many it’s a sincere belief. A Sister Souljah moment could never happen today for a white male Democratic politician because he would be accused of being a white supremacist for attacking a black woman (Obama himself was attacked for pandering to ‘respectability politics’).

On immigration, note that in the mid-2000s Republicans could have probably been able to muster the courage to ignore the base if the Democrats had agreed to a bill to flood this country with high skilled immigration (a proposal by some Republicans). But for political and policy reasons the Democrats wanted something comprehensive, which includes lower skilled workers who are both the Democrats’ future vote bank, and people who are important (often relatives) to Democratic voters.

Above Drum asks about conservatives and which views they keep quiet about in relation to policy. I think there is more variation on responses to climate change, foreign policy, and tax policy than you might think. The fear comes not from the social media mobs, but from the wealth people and interest groups funding fellowships.

About ten years ago Reiham Salam and Ross Douthat wrote Grand New Party in part to stake out a fiscally more moderate and socially conservat(ish) framework. There are obviously a lot of voters in that position, but the donor class was never a big fan. Trump seems to have taken that plank in a more populist direction and run with it, but there doesn’t seem to be the policy and personnel infrastructure to execute on this, so you see a more donor class friendly presidency (at least so far).

The Evolution meeting is happening right now in Portland. Check out the hashtag, #evol2017.

California just added four more ‘discriminatory’ states to its travel ban. This is going to impact academics in the UC system who may want to visit UT or UNC or Duke. As a friend pointed out the state of California is really punishing the blue areas of red states, since these are the places which interact the most with California. I think this is just BDS thinking spreading. It may trigger counter proposals, but as I said the people most impacted in red states are Democrats. Perhaps there won’t be any reaction? Like economic sanctions on authoritarian states this is going to hurt people you don’t want to hurt, without impacting the people you are targeting. But it makes you feel good.

Happy Eid.

In case you haven’t noticed I’ve been posting on Brown Pundits a fair amount.

The assumption of pulse admixtures is easy, but it’s often wrong. I really hope this gets more wide circulation because it might be leading us astray in many ways. Though this varies by taxa. Plants probably have less pulse admixture going on that social organisms.

In Turkey, No Teaching Of Evolution, But Banning Gays Is Fine. It’s hard to gauge Erdogan sometimes, because he made some liberal(ish) noises as late as the Arab Spring in 2011. No longer.

Translating Genesis. Alter’s translation and commentary is my favorite so far, but it’s been many years since I read Genesis. Any good recommendations? (please don’t say NIV)

New job.

Enrichment of low-frequency functional variants revealed by whole-genome sequencing of multiple isolated European populations.

Draft genome of the Reindeer (Rangifer tarandus). Huge on Sami Twitter.

Savarkar’s book Hindutva needs a new cover.

A former executive is accusing Infosys of racism that favours Indians #whiteSupremacy.

Genetic loci associated with coronary artery disease harbor evidence of selection and antagonistic pleiotropy. Not a huge surprise.

Did I mention SciReader is back?

Estimates of Introgression as a Function of Pairwise Distances.

Leaderless Uber Scrambles to Prevent Employee Exodus. I think if Netflix ever stumbles they’ll have enormous issues immediately, since their hiring and firing policy puts zero emphasis on loyalty.

US court grants Elsevier millions in damages from Sci-Hub. If you don’t know about Sci-Hub, read the article.

Robots That Make 400 Burgers an Hour May Soon Take over Fast Food Restaurants. Burger meat is usually the low quality stuff. I suspect a combination of lab grown meat and/or vegan meat-substitute is going to come to dominate the market in a generation. Combined with automated burger making a whole sector will be transformed (in contrast, steaks require a lot more work to imitate, so people will probably eat real meat steaks for a while).

Natural selection shaped the rise and fall of passenger pigeon genomic diversity.

Revenge of the scaly Tyrannosaurus.

June 24, 2017

We need more housing for the upper upper middle class

Filed under: Culture,Housing — Razib Khan @ 9:46 pm
$1.5 million dollar house in Palo Alto

When people talk about real estate affordability and gentrification often the focus is on housing for the poor. Myself, I don’t think this is the issue. People with means wouldn’t move into poor neighborhoods if there was housing they could afford elsewhere.

Most of the “multi-million dollar” houses in Palo Alto are not mansions. Many are not really worth that much because of the house; it’s just the land. These are modest homes which really are appropriate for middle class buyers. In fact they were often built with middle class buyers in mind.

But in places like Palo Alto they are now for two types of people: long-term residents (who also likely don’t pay much property tax), and those with very high incomes and/or wealth due to selling companies.

From an article published last year:

The average price of the Palo Alto homes that went on the market today is just over $3 million. With a 20 percent down payment and the state’s average 30-year fixed mortgage rate of 3.77 percent, the average monthly payment on those homes would be a little over $14,000, two-thirds of the monthly income for a quarter-million dollar household.

It’s hard to imagine that two married Google engineers in their twenties could afford a house in Palo Alto. It’s beyond their means. But these homes are not luxurious in and of themselves. They’re all that the upper upper middle class have access to nearby.

In Silicon Valley they love to reimagine stuff. But only some people like the demi-god Elon Musk are focusing on concrete things, like cars and rockets. They need to re-imagine housing. There’s no reason the people coding the future should live in post-war ranch homes.

The pork episode of Master of None

Filed under: Aziz Ansari,Religion — Razib Khan @ 7:14 pm


The Aerogram has a piece out, Bacon & (Un)Belief: Religion & American Secularism in Master of None, which reviews The Master of None episode about religion. I kind of agree that it was a little unbelievable in relation to his cousin, and how quickly he became a porkoholic.

That being said I think it is important to note a personal aspect of Aziz Ansari’s relationship to religion. Here’s a correction to an article in The New York Times profiling Aziz:

In an earlier version of this article, Michael Schur, the co-creator of “Parks and Recreation,” partly described Mr. Ansari as a Muslim. Mr. Ansari describes himself as an atheist.

Aziz Ansari does not define himself from what I can tell as a bad or liberal Muslim. He says he’s not religious. He happens to be a guy who is an atheist, a very negatively viewed group, who is from a Muslim background a very negatively viewed group. That is one way we have a lot in common.

Also, I had a bacon experience very similar to Aziz. Though in my case it was at a friend’s house where they were Hindus from West Bengal, and my friend was having bacon. My mom came over and I had a piece of bacon in my mouth. She was a little chagrined though she said I’m not supposed to eat pork products.

In general I still don’t eat much pork and ham. But I really love bacon, and have no problem with pork sausages.

Hasan Minhaj and Aziz Ansari: your race defines you and it doesn’t

Filed under: Aziz Ansari,Comedy,Film,Hasan Mihnaj — Razib Khan @ 4:31 pm

Today I watched Homecoming King, a comedy show by Hasan Minhaj. Honestly I wasn’t going to watch it, because Minhaj’s political schtick at The Daily Show was not geared toward someone like me. That is, it’s funny to laugh along with him, but it is much easier if you agree with him politically. To me this is a major contrast with Aziz Ansari, who probably shares most of the politics of Minhaj, but who does not seem to foreground it as much.

Some of this is happenstance. Minhaj blew up on The Daily Show, which focused on politics with a liberal slant. Ansari became more well known through episodic television. That’s going to impact the sort of comedy they put out there.

But after watching Minhaj outside of The Daily Show context, and comparing his routine to Aziz Ansari’s (I’ve also watched much of Master of None), I think it is notable how differently they come off despite the likelihood that on the fundamentals they probably agree about much in American society. In short, Minhaj’s experience and recollection of racism seems much more raw to me than Ansari, who seems to have taken it more in stride.

I was encouraged to watch Homecoming King  in part because Minhaj grew up in Davis, California. I lived there for five years and one of my closest friends during my undergraduate years is a Davis native. In fact I went to her wedding in Davis during Minhaj’s senior year in high school. The centerpiece of Homecoming King happens to be about an event before prom which involved racism of a subtle but hurtful form that traumatized him in a very deep fashion. He’s talked about this incident extensively so you can Google it. But it colors all of Homecoming King.

But there are some differences between Ansari and Minhaj which I think require highlighting. Ansari is 5’6 feet tall, while Minhaj is 6’0 feet tall. Ansari is also darker-skinned, and I think I can say he is less conventionally attractive than Minhaj (readers who are attracted to men can correct me here). Finally, Minhaj grew up in very liberal Davis, California, situated between the Bay Area and Sacramento. Ansari grew up in a small town in South Carolina. I suspect that Ansari probably faced more racism than Mihnaj when he was growing up if I had to bet.

And yet of the two Aziz Ansari seems to be less deeply impacted by the banal ubiquity of white American racism. He acknowledges that it exists, sometimes in a pointed fashion. But he does not seem to let it define him.

In  Homecoming King Minhaj’s trauma from his abortive relationship with a white girlfriend scars him so much that he says he could not date white girls after that. In contrast I’m sure Ansari has experienced some level of racism against him on the dating scene. Especially in the South where when he was growing up interracial relationships were probably more taboo than in Davis. It comes up a few times in Master of None, but it’s not defining in any way. He keeps on trying to find someone he can connect with no matter their race, even if “on paper” they should be out of reach for a short dark sinned guy.

Finally, this is a minor thing, but Ansari is more explicitly disconnected from his Muslim background. He has stated he is an atheist to the media. One episode of Master of None involves him eating pork in front of his parents. Minhaj in contrast seems to own his Muslim identity much more (albeit, of a very liberal cultural variety).

Rather than being exemplars of young brown men in the United States, the subtle differences between Ansari and Minhaj show that there isn’t one way to be brown, and that we aren’t impacted in the same way by how society views us. Like Minhaj I went to high school where I was the only brown kid. Also, like Minhaj I was called Saddam Hussein. Unlike Minhaj my town was overwhelmingly conservative, while his was overwhelmingly liberal. While my town was over 90 percent white (actually more than 95 percent when I went to high school since I’m about 10 years older than Minhaj), his was about 70 percent white. What was the difference between us? A lot of it comes down to personality.

Some liberals of a minority background feel besieged by the white majority. In contrast, many of us who are more conservative accept racism is part of life, but move on, and don’t believe it is as determinative as liberals assert. Much of this comes down to personality differences, rather than race differences. Minhaj and Ansari are both successful politically liberal Indian American comedians from a Muslim background. But how they experienced American society and present themselves still differences because they are still individuals with all the differences that entails.

Indian genetics, part n of many

Filed under: ancient india,History,Indo-Europeans — Razib Khan @ 2:59 pm

I put up close to definitive piece for me in relation to South Asian historical population genetics. At least until new research is published. I did leave out some stuff about my own vague thoughts…but I think the takeover of Hattian and Hurrian cultures by the Nesha (Hittites) and Haryannu (Mitanni) have something to teach us….

Indian genetic history: before the storm

Filed under: Genetics,History,India — Razib Khan @ 2:52 pm

Over at Brown Pundits I’ve mentioned the continuing simmer of controversy over a recent piece, How genetics is settling the Aryan migration debate. This has prompted responses in the Indian media from a Hindu nationalist perspective. One of these notes that the author of the piece above cites me, and then goes on to observe I was fired from The New York Times a few years ago due to accusations of racism (also, there is the implication that I’m just a blogger and we should trust researchers with credibility like Gyaneshwer Chaubey; well, perhaps he should know that Gyaneshwer Chaubey considers me “unbiased” according to an email exchange which I had with him last week [we all have biases, so I think he’s wrong in a literal sense]).

I was a little surprised that a right-wing magazine would lend legitimacy to the slanders of social justice warriors, but this is the world we live in. Those who believe that everything written about me in the media, I invite you to submit your name and background to me. I have contacts in the media and can get things written if I so choose. Watch me write something which is mostly fact, but can easily misinterpreted by those who Google you, and watch how much you value the objective “truth-telling” power of the press.

There’s a reason so many of us detest vast swaths of the media, though to be fair we the public give people who don’t make much money a great deal of power to engage in propaganda. Should we be surprised they sensationalize and misrepresent with no guilt or shame? I have seen most of those who snipe at me in the comments disappear once I tell them that I know what their real identity is. Most humans are cowards. I have put some evidence into the public record to suggest that I’m not.

Perhaps more strange for me is that the above piece was passed around favorably by Sanjeev Sanyal, who I was on friendly terms with (we had dinner & drinks in Brooklyn a few years back). I asked him about the slander in the piece and he unfollowed me on Twitter (a friend of Hindu nationalist bent asked Sanjeev on Facebook about the articles’ attack on me, but the comment was deleted). It shows how strongly people feel about these issues.

I’m in a weird position because I’m brown and have a deep interest in Indian history. But that interest in Indian history isn’t because I’m brown, I’m pretty interested in all the major zones of the Old World Oikoumene. Aside from some jocular R1a1a chauvinism I don’t have much investment personally (I just told said Hindu nationalist friend who turns out to be R2 to clean my latrine; joking of course, though I’m sure he resents that I’m descended on the direct paternal line from the All-Father & Lord of the Steppes and he is not!).

In the aughts I accepted the model outlined in 2006’s The Genetic Heritage of the Earliest Settlers Persists Both in Indian Tribal and Caste Populations. But to be frank it always struck me as a little confusing because the tentative autosomal data we had suggested that many South Asians were closer to West Eurasians than deep divergences dating to the Last Glacial Maximum would suggest. Since I’ve written something like 5 million words in 15 years, I actually can check if I’m remembering correctly. So here’s a post from 2008 where I express reservations of the idea of long term deep heritage of Indians separate from other West Eurasians. The reason I was so impressed by 2009’s Reconstructing Indian Population History is that it resolved the paradox of South Asian genetic relatedness.

To recap, Reich et al. proposed that modern Indians (South Asians) could be modeled as a two way mixture between two distinct populations with separate evolutionary genetic histories, Ancestral North Indians and Ancestral South Indians (ANI and ASI). How distinct? ANI were basically another West Eurasian population, while ASI was likely nested in the clade with Eastern Non-Africans. Additionally, there was a NW-to-SE and caste admixture cline. In other words, the higher you were on the caste ladder the more ANI you had, and the further your ancestors were from the north and west, and more ANI you had. The difference between Y and mtDNA, male and female, could be explained by sex-biased migration.

But there were still aspects of the paper which I had reservations about. After all, it was a model.

  • Models are imperfect fits onto reality. The idea of mass migration seemed ridiculous to me at the time, because even by the time of the Classical Greeks it was noted that Indian was reputedly the most populous land in the world (to their knowledge). But ancient DNA has convinced me of the reality of mass migrations.
  • I wasn’t sure about the nature of the closest modern populations to the ANI. The researchers themselves (in particular, Nick Patterson) told me that the relatedness of ANI to Europeans was very close (on the order of intra-European differences). But modern Indians do not look to be descended from a population that is half Northern European physically. Again, ancient DNA has shown that there was lots of population turnover, and it turns out that Europeans and ANI were likely both compounds and mixed daughter populations of common ancestors (also, typical European physical appearance seems to emerged in situ over the past 5,000 years).
  • The two way admixture modeled seemed too simple. I had run some data and it struck me that North Indian populations like Jats had something different than South Indian groups like Pulayars. In 2013 Priya Moorjani’s paper pretty much confirmed that it was more than a two way admixture along the ANI-ASI cline.

This March BMC Evolution Biology published Silva et al’s A genetic chronology for the Indian Subcontinent points to heavily sex-biased dispersals. It has made a huge splash in India, arguably triggering the write up in The Hindu. But for me it was a bit ho-hum. If you read my 2008 post it is pretty clear that I suspected the most general of the findings in this paper at least 10 years back. It is nice to get confirmation of what you suspect, but I’m more interested to be surprised by something novel.

Nevertheless A genetic chronology for the Indian Subcontinent points to heavily sex-biased dispersals has come in for lots of repeated attack in the right-wing Indian press. This is unfair, because it is a rather good paper. I suspect that it wasn’t published in a higher ranked journal because most scientists don’t consider the history of India to be that important, and they didn’t really apply new methods, as opposed to bringing a bunch of data and methods together (in contrast, the 2009 Reich et al. paper was one of the first publications which showed how to utilize “ghost populations” in explicit phylogenetic models with relevance to human demographic history).

As it happens I will be writing up my thoughts in detail in an article for a major Indian publication (similar circulation numbers as The Hindu). This has been in talks for over six months, but I’ve been busy. But a month or so ago I thought it was time that I put something into print for the Indian audience, because I felt there was some misrepresentation going on (i.e., the Aryan invasion theory has been been refuted by genetics, but this is what many Indians assert).

For any years people have told me there are certain topics that shouldn’t be talked about. I have offended people greatly. There are many things people do not want to know. I have come to the conclusion this is not an entirely indefensible viewpoint (though if you accept this viewpoint, I think acceptance of authoritarianism is inevitable, so I hope people will toe the line when the new order arrives; knowing their personalities I think they will conform fine). But my nature is such that I continue to have nothing but contempt for the duplicitous and craven manner in which people go about these sorts of private conversations. I assume that as someone with the name “Razib Khan” I will be attacked vociferously by Hindu nationalists, who will no doubt make recourse to the Left-wing hit pieces against me to undermine my credibility. The fact that these groups are fellow travelers should tell us something, though I will leave that as an exercise for the reader.

I will write my piece that reflects the science as I believe it is, without much consideration of the attacks. That is rather easy for me to do in part because I live in the United States, where denigrating the deeply held views and self-esteem of Hindu nationalists is not sensitive or politically protected (unlike say, Muslims). And Hindu nationalists are less likely to kill me by orders of magnitude than Muslim radicals, and they have far less purchase in this nation then the latter (though you may be interested to know that very conservative Muslims follow me on Twitter; they’re actually more open-minded than many SJWs to be entirely honest).

Let me go over some general points that I see coming up over and over on the relationship between Indian (pre)history and genetics in the critiques .

One of the major critiques has to do with the nature of R1a-Z93 and its subclades. Basically this Y chromosomal haplogroup, the greatest that has ever been known, exhibits a strong signature of very rapid expansion over the past 4,000 years or so. It is divided from Z282. While Z93 is found in South Asia, Central Asia, and Siberia, Z282 is European, with its dominant subclade the one associated with Eastern Europeans. Both of these clades of R1a have gone through massive expansion. In the Altai region R1a is 40% of the heritage of peoples who are now predominantly East Eurasian today. But they are Z93. Additionally, ancient DNA from the Pontic Steppe dated ~4,000 years ago from Srubna remains is Z93, as are Scythian remains from the Iron Age.

Much of the argument comes down to dating, and citing papers that give deep coalescence numbers between difference branches of R1a1a. Hindu nationalists and their fellow travelers point to recent papers which give dates >10,000 years ago, and so place the origin of Z93 plausibly in the Pleistocene. The problem is that Y chromosomal coalescence dating is something of a mug’s game. Often they use microsatellite data whose mutational rates are highly uncertain. In contrast, using SNP data, which has a slower mutation rate but requires a lot more data, you get TRMCA (common ancestry) between Z93 and Z282 around ~5,800 years ago. But coalescence estimates often have wide confidence intervals of thousands of years. And even with these intervals, the assumptions you make (e.g., mutation rate) strongly influence your midpoint estimate.

The Y chromosomal data is powerful, but its interpretation is still buttressed upon other assumptions. The really big picture framework is the nature of ancient genome-wide variation across Eurasia. Lazaridis et al. 2016 condition us to a prior where much of Eurasia was subject to massive population-wide genetic changes since the Holocene. Therefore, I am much less surprised if there was massive genetic change in India relatively recently. The methods in Priya Moorjani’s paper and in other publications make it obvious that mixture was extensive in South Asia between very distinct groups until about ~2,000 years ago. In fact, Moorjani et al. using patterns of variation across the genome to come at a number of two to four thousand years ago as the period of massive admixture.

Though we don’t have relevant ancient DNA from India proper to answer any questions yet, we do have ancient DNA from across much of Europe, Central Asia, and the Near East. What they show is that Indian populations share ancestry from both Neolithic Iranians and peoples of the Pontic steppe, who flourished ~5 to ~10,000 years ago. To some extent the latter population is a daughter population of the former…which makes things complicated. Conversely, no West Eurasian population seems to harbor ancient signals of ASI ancestry.

One scientist who holds to the position that most South Asian ancestry dates to the Pleistocene argued to me that we don’t know if ancient Indian samples from the northwest won’t share even more ancestry than the Iranian Neolithic and Pontic steppe samples. In other words, ANI was part of some genetic continuum that extended to the west and north. This is possible, but I do not find it plausible.

The reasons are threefold. First, it doesn’t seem that continuous isolation-by-distance works across huge and rugged regions of Central Eurasia. Rather, there are demographic revolutions, and then relative stasis as the new social-cultural environment crystallizes. This inference I’m making from ancient DNA and extrapolating. This may be wrong, but I would bet I’m not off base here.

Second, it strikes me as implausible that there was literally apartheid between ASI and ANI populations for the whole Holocene right up until ~4,000 years before the present. That is, if Northwest India was involved in reciprocal gene flow with the rest of Eurasia over thousands of years I expect there should have been some distinctive South Asian ASI-like ancestry in the ancient DNA we have. We do not see it.

Third, one of the populations with strong affinities to some Indian populations are those of the Pontic steppe. But we know that this group itself is a compound of admixture that arose 5,000-6,000 years ago. Because of the complexity of the likely population model of ANI this is not definitive, but it seems strange to imagine that ANI could have predated one of the populations with which it was in genetic continuum as part of a quasi-panmictic deme.

Finally, many of the critiques involve evaluation of the scientific literature in this field. Unfortunately this is hard to do from the outside. Citing papers from the aughts, for example, is not wrong, but evolutionary human population genomics is such a fast moving field that even papers published a few years ago are often out of date.

Many are citing a 2012 paper by a respected group which argues for the dominant model of the aughts (marginal population movement into South Asia). One of their arguments, that Central Asian migrant should have East Asian ancestry, is a red herring since it is well known that this dates to the last ~2,000 years or so (we know more now with ancient DNA). But the second point that is more persuasive in the paper is that when they look at local ancestry of ANI vs. ASI in modern Indians, the ANI haplotypes are more diverse than West Eurasians, indicating that they are  not descendants but rather antecedents (usually the direction of ancestry is from more divers to less due to subsampling).

There are two points that I have make here. First, local ancestry analysis is difficult, so I would not be surprised if they integrated ASI regions into ANI and so elevated the diversity in that way (though they think they’ve taken care of it in the paper). Second, if the ANI are a compound of several West Eurasian groups then we expect them to be more diverse than their parents. In other words, the paper is refuting a model which is almost certainly incorrect, but the alternative hypothesis is not necessarily the one they are supporting within the paper.

But there are many things we do not know still. Many free variables which we haven’t nailed down. Here are some major points:

  • Y chromosomal lineages have a correlation with ethno-linguistic groups, but the correlation is imperfect. R1b and R1a seems correlated with Indo-European groups, but both these are found in high proportions in groups which are putatively most “pre-Indo-European” in origin (e.g., Basques, Sardinians, and South Indian tribals and non-Brahmin Dravidian speaking groups). Also, haplogroups like I1 in Europe expands with Indo-Europeans locally, suggesting there was lots of heterogeneity in Indo-Europeans as they expanded. In other words, Indo-European expansion in relation to powerful paternal lineages did not always correlate with ethno-linguistic change.
  • There are probably at minimum two Holocene intrusions from the northwest into South Asia, but this is a floor. The models that are constructed always lack power to detect more complexity. E.g., it is not impossible that there were several migrations of Indo-Europeans into South Asia which we can not distinguish genetically over a period of a few thousand years.
  • If one looks over all of South Asia it may be that ASI ancestry in totality is >50% of the total genome ancestry. I haven’t have a good guess of the numbers. If this is correct, perhaps most South Asian ancestors 10,000 years ago were living in South Asia (though the fertility rate are such in Pakistan that ANI ancestry is increasing right now in relative rates).
  • But, this presupposes that ASI were present in South Asia in totality 10,000 years ago, rather than being migrants themselves. If ancient DNA confirms that ANI were long present in Northwest India, I hold then it is entirely likely that ASI was intrusive to South Asia! The BMC Evolutionary Biology Paper does a lot of interpretation of deep structure in haplogroup M in South Asia. I’m moderately skeptical of this. Europe may not be a good model for South Asia, but there we see lots of Pleistocene turnover.

So where does this leave us? Ancient DNA will answer a lot of questions. Pretty much all scientists I’ve talked to agree on this. My predictions, some of which I’ve made before:

  1. The first period of admixture is old, and dates to the founding of Mehrgarh as an agricultural settlement. The dominant ANI component dates to this period and mixture event, all across South Asia. The presence in South India is due to expansion of these farming populations.
  2. A second admixture event occurred with the arrival of steppe people. Those who argue for the Aryan invasion model posit 1500 BCE as the date. But these people probably were expanding in some form before this date.
  3. We still don’t know who the antecedents for the Indo-Aryans were. Probably they were a compound of different steppe groups, and also other populations which were mixed in (by analogy, in Europe it is obvious now that there was some mixture with the local European farmers and hunter-gatherers as Europeans expanded their frontier westward; the same probably applies for Indo-Aryans are the BMAC).

June 22, 2017

Nearly 20% of McDonald’s will have electronic kiosks by the end of 2017

Filed under: Economics — Razib Khan @ 9:56 pm


McDonald’s hits all-time high as Wall Street cheers replacement of cashiers with kiosks:

Andrew Charles from Cowen cited plans for the restaurant chain to roll out mobile ordering across 14,000 U.S. locations by the end of 2017. The technology upgrades, part of what McDonald’s calls “Experience of the Future,” includes digital ordering kiosks that will be offered in 2,500 restaurants by the end of the year and table delivery.

There are 14,500 locations. Right now 500 stores have kiosks.

June 21, 2017

American cities need to grow up to solve the housing crisis

Filed under: Culture,Housing Crisis — Razib Khan @ 7:51 pm

Martin Jacques observes in When China Rules the World that East Asian cities don’t have the organically evolved feel of European urban areas. He chalks this up to the rapid economic development of the “Asian Tigers” and Japan over the past few decades. Buildings were built, buildings were torn down. The rate of change didn’t allow for the accumulation of historical authenticity. There’s also another reason: many East Asian societies have built buildings out of perishable materials like wood and so not prized historicity of structures.

The oldest free standing timber building in China dates to 782. The Songyue Pagoda dates to 523, but it’s made of brick. In contrast great public buildings made of marble still exist in the Western world that date back to antiquity. The Pantheon became a church and so is preserved in nearly its full glory. Public buildings and historical architecture are great. But the valorization of the principle can come at a price.

Willamette Week has an article up on the attempt to “maintain historic character,” and how it prevents the emergence of affordable housing. Portland’s Laurelhurst Neighborhood Fights to Keep the Housing Crisis Out:

At the end of last month, residents of Laurelhurst turned out in record numbers to vote in their neighborhood association election for one reason: to get protection from developers.

The winning candidates pledged to bypass City Hall and ask the National Park Service to declare much of the 425-acre eastside neighborhood a historic site.

By being labeled “historic” the residents can block development, and preserve the state of their neighborhood the way they like it. They are very explicit about what they want to do:

By seeking to make the neighborhood a historic district, Laurelhurst residents are taking aim at what they see as the neighborhood’s greatest enemy: a real estate developer with a backhoe, bent on tearing down 100-year-old houses to replace them with apartments, a duplex or a huge new house.

“The whole street—it will look like Beaverton by the time they’re done,” says John Deodato, a longtime Laurelhurst homeowner who says he gets 20 letters a month from developers seeking to buy his home. “The city won’t do anything about it unless we do.”

Beaverton is a suburb of Portland. Though the analogy is imperfect, if Portland is West LA, Beaverton is Irvine. The connotation of this insult is clear to any Oregonian. It’s a sneer at those without refined sophistication and breeding.

Laurelhurst has a 14 to 1 Democrat to Repubican ratio, and median home value is $750,000. The median household income for the greater Portland area is $65,000. The median home value in Beaverton is about $360,000. I looked at Zillow and found an $800,000 home in Laurelhurst. You can see that it has appreciated nicely over the last 10 years.

The recent neighborhood association seats were contested. The outcomes were clear:

More than 800 people voted in the election—a record for the neighborhood, and more than 10 times the number of voters in the previous election. The vote went overwhelmingly for the historic district candidates. Pratt, the pro-historic district candidate for president, won just under 80 percent of the vote.

It is no surprise that the people who live in Laurelhurst are voting to protect their interests. Their implicit gated community, with its high property values. They may be progressive in their avowed values, but when their self-interest is at state, they make sure to take care of their self-interest and conserve what they have the way they like it.

There are of opponents to this trend of gentrified Portland neighborhoods. They profile an alliance between a developer and the head of 1000 Friends of Oregon, a nonprofit which favors density over sprawl. Below is some of their rationale, along with what someone in Laurelhurst has to say about these men:

“The reasons we are involved with this bill has nothing to do with whether the home builders are involved with it,” says McCurdy. “The bill increases housing opportunities—diverse housing opportunities and affordable housing opportunities—all of those inside our towns and cities, which is part of the land-use deal that we as Oregonians have had in place for 40 years.”

McCurdy believes what’s happening in Laurelhurst is a “misuse of historic district designation to prevent change.”

Critics of the bill call 1000 Friends’ and the home builders’ support an unholy alliance.

“Gov. McCall would be spinning in his grave to see his beloved 1000 Friends of Oregon organization working side-by-side with the Home Builders Association, buying into the alt-right, fake-news theory of demolition as the cure for affordability,” wrote Tracy Prince, vice president of the Goose Hollow Foothills League, in a May 17 letter to legislators.

In the early 2000s anything and anyone that self-styled progressives did not like was “neocon.” Today it is “alt-right.” Somehow this woman believes that allowing for development which would allow for an increase in the local housing supply and destroy some of the quaint town-like character of East Portland streets is “alt-right.” If she lived in the 1950s I wonder if she would accuse her enemies of being “Communists.”

The article has a definite slant against the Laurelhurst neighborhood association. The author of the piece lives in Northeast Portland, so she’s able to see through the pleading for the “special character” of Laurelhurst (in fact, records indicate that she is a recent transplant to the city from New York City, so her sympathies are likely not with the old-timers). At one point the author interviews a man who is living out of his pickup truck in Laurelhurst. He’s making $12 an hour, and couldn’t afford a place elsewhere in Portland, let alone Laurelhurst. She notes that “A Craigslist ad posted last week shows a restored attic in this neighborhood renting for $1,000 a month” in the neighborhood.

The piece concludes:

Pratt, the neighborhood association president, knows plenty about homelessness. A couple years ago, he served on the board of social services agency JOIN, which coordinates shelter beds.

Pratt acknowledges Portland needs to build more housing. But not too much of it in Laurelhurst.

“Everybody says the solution to homelessness is housing,” he says. “I don’t think the solution is that every neighborhood looks the same, and every neighborhood has everything, and your neighborhood [has] no uniqueness anymore.”

People have interests. But they don’t want to admit those interests in public. The Laurelhurst neighborhood association’s attempt to gain historic designation is regulatory arbitrage. They want to preserve their neighborhood and property values, and not let in the riff-raff have any space. Earlier in the piece there is a quote from the association president: “Pratt warns that if Laurelhurst isn’t allowed to decide what gets developed within its boundaries, the neighborhood will indeed become cheaper eventually—because it will become hideous.

Beauty is important. It has value. But if we need to sacrifice beauty for affordability, at some point the latter does have to overrule the former.

The political Left on the national level is at least waking up to the problem. Recently Mother Jones wrote Berkeley Says It’s Standing Up to Trump, But It’s Actually Busy Arguing About Zucchini. The title comes from this passage:

At Tuesday night’s city council meeting, which touched on a number of housing issues, this dissonance was on display in a resident’s complaint about a proposed new building that would cast shadows on her zucchini plants. The project was returned to the city’s Zoning Adjustments Board. The zukes live another day.

“Delaying or denying housing approvals suggests to Berkeley neighbors that their stalling tactics will work, and invites more of them in the future,” web developer Kevin Burke wrote in a letter to the council after the meeting, expressing his disappointment with the decision. “I would also much rather have a zucchini garden crisis than a housing crisis.”

The gut-punch is that an anti-development mayor has been elected in Berkeley. How “radical.” In San Francisco and San Mateo counties $105,000 a year for a household of four is low income. The average household income in San Francisco happens to be $105,000 per year.

Yesterday and today on Twitter there was a discussion about post-doc salaries. To a great extent this is a stage in academic life when the salary range is compressed because there are broad national guidelines and expectations. The median post-doc makes $46,000. The 10th percentile is $37,000, and the 90th percentile is $65,000.

So let’s compare some universities and their locales. In US News Stanford has the #2 genetics graduate program and Washington University in St. Louis the #5 program.

According to a cost of living calculator a “salary of $50,000 in St. Louis, Missouri should increase to $304,167 in Palo Alto, California.” This is because housing is 24 times more expensive in Palo Alto. So a hypothetical post-doc at Stanford that is paid $100,000 is equivalent to $16,000 in St. Louis. You might object that Palo Alto to St. Louis is apples to oranges, but the housing expense in the greater Bay Area means that you can’t just escape Palo Alto for relief. A Zillow check of Washington University vs. Stanford shows that houses within walking distance of the latter university are about 15 times more expensive than the former. The average assistant professor at Washington University has a salary in the low $100,000 range. At Stanford it is in the mid-$100,000 range. Basically a Stanford assistant professor makes about 1.5 times more in salary than a Washington University assistant professor, even though cost of living is going to be 6 times greater in Palo Alto.

At this point I could go into tangents about university housing for post-docs and faculty in the Bay Area (one of my friends is doing a post-doc at UCSF and had to have a subsidized apartment for obvious reasons). And obviously opportunities for consulting are more available in the Bay Area. But the point is not about academics and their careers. Rather, I’m using an illustration of the circumstances in which “winners” in American society, people with lot of higher education, can find themselves in financial stress.

There are genuine benefits of starting a career in the Bay Area. For an academic you have access to world-class institutions, with the Stanford, UCSF and Berkeley triangle, and UC Davis and UC Santa Cruz just beyond the horizon, and other institutions like San Francisco State to fill out the landscape. For a techie you know where the “action” is. If you are a single person, a $125,000 salary at Google won’t allow to you live luxuriously, but you can survive. Hopefully you’ll be able to make connections that help you later on, when you inevitably have to ask for a transfer because you want a house and a family.

This is the cycle of life now. But not for everyone. I lived in California for almost ten years, and there are those to the Golden State born whose families bought homes decades ago. The property tax regulations California are Byzantine, but there are plenty of cases where individuals are “grandfathered in” and pay very little tax on a very valuable property. And, these benefits can pass on to children. In other words you may have millennials paying tax rates on million dollar homes that date back to assessments in the 1970s, when their parents owned the house.

We can debate the merits of this system. One can make a case for giving those with deep lineage in an area privileges over newcomers. I lived in a house in Berkeley where the property owner told me once that he paid on the order of 15 times less tax than his neighbor, because the house had been in the family for 60 years. It was purchased by his grandparents, and owned by his mother, and it had passed on to him. His profession was as a part-time photographer and musician. Because his tax bills were so modest he could rent out rooms in the house and and survive in Berkeley even though his non-property income was irregular and not particularly high (when I lived in his house he would complain that he didn’t want to purchase health insurance due to the cost).

For those of us without those privileges if we want to live in the urban areas where our specialized skills return the greatest income and also where we can network and grow our career the best, we need to make sacrifices. For many people that means putting off getting married, putting off having children. Anyone who makes less than $100,000 a year will probably have to hustle in Silicon Valley. There are flophouses from San Francisco down to San Jose where young people of more modest means live together in a communal fashion in dormitories.

How did we get here? I think I’ve outlined a major part of how we got here. Many places people want to live are extremely expensive because supply of housing is constrained.

Houston has a great food scene, but quaint and charming is not something anyone would say about it. But it is very affordable. And, the fourth largest city in this country. It lacks zoning. In contrast San Francisco is beautiful. There is something special about it, from the feces on the sidewalks in the Tenderloin to the beauty of the Golden Gate bridge. Something would be lost if one allowed it to develop vertically. But do we want the city to become a playground for the wealthy and those born into old families of the city? Because that’s what’s happening with the choices we’re making in this country.

Our vision for the future used to be optimistic. We would live better. We would be space age humans. Much of it has come to pass. Our “phones” are amazing things. Electric driverless cars will transform our cities within the next generation. But the way we do housing in this country has not moved much beyond the middle of the 20th century. We need changes in culture, changes in technology, to make things better for future generations, rather than constraining them with the paltry opportunities of the present.

June 20, 2017

Liberals will never disappear (neither will atheists)

Filed under: Behavior Genetcs,Behavior Genetics — Razib Khan @ 1:33 am

In Quillette Hrishikesh Joshi and Jonny Anomaly* ask Are Liberals Dying Out? Since the piece has been shared a fair amount (judging by my Twitter timeline), I thought I should respond to why I don’t think that is a major concern. Let me jump to their last paragraph:

Nevertheless, despite cultural trends, the best available evidence suggests that political ideology is heritable, and that people with liberal personality traits currently have far fewer children than conservatives. If this trend continues, it is possible that the reproductive choices people are making today will influence the political climate of future generations. Over the long run, conservatives could end up winning the ideological contest with fertility rather than arguments.

First, I don’t think the title reflects the modest contentions of the piece. I beseech the editors of Quillette to not engage in the titular hyperbole so common in the mainstream media!

I agree that political orientation seems heritable. That is clear in books like Born That Way. But heritability expresses itself in an environmental context. If you had a totalitarian government most of the phenotypic variation would disappear. Yes, there would be dissidents, but they’d be freaks. Most humans would conform (no, I don’t think the citizens of Soviet Russia were genetic freaks unable to grasp freedom like Howard Roark). The correlation between religiosity and fertility varies by society as well. The more secular the society, the bigger the gap (though last I checked this was not true in China). In a totally conservative future heritable variation for liberalism could just reemerge.

Second, political orientation exists on a relative plane. If one imagines it as some specific thing, or disposition, one can imagine that in the future the liberal-conservative spectrum would exist, but just be shifted. Quantitative genetics has shown that selection can move the mean many standard deviations. I don’t think this is a strong objection to their overall point, but it gets at the fact that we view liberal-conservative tendencies along a distribution (1980s liberal commentator Jeff Greenfield was widely known for making disparaging comments about gays i the prime of his career; that did not destroy his career as a liberal pundit at that time). Perhaps liberal have already won in an age when most conservatives understand and accept that gay marriage is here to stay.

Third, some of the variation is not heritable. It’s random. In fact around half of it within the population. Some people may just be liberal for stochastic reasons. You aren’t going to get rid of this with selection.

Perhaps most essential in terms of theory: frequency dependence. The dynamics of human interaction and decision making are such that the frequency of liberals declining might have an impact on their fitness. To give a weird example, perhaps an economically post-Malthusian society needs a certain number of sub-replacement liberals who engage in particularly productive work to maintain itself. If society slouched rapidly back toward Malthusianism perhaps everyone would just trudge along at replacement.

The big picture problem is assuming constant directional selection and exhaustion of heritable variation is all well and good when you are selecting for wax-seed oil, but human societies are non-linear systems which are subject to big shocks. They aren’t controlled agricultural genetic experiments.

Finally, let me use an analogous case to make an empirical objection. Many people tell me that the future will be religious due to the same dynamics above. This despite the century long trend toward secularization (parenthetical, God is Back was an ill-timed books, as the United States was shifting toward secularization at that time).

But I want to go back further. France was the first nation to start the demographic transition. In the early 19th century the secular elite was worried about the fertility of devout Roman Catholics, in particular the Poles who were arriving. The secular future they envisioned was threatened. It’s been nearly 200 years since these worries, and in those 200 years France has become more and more secular.

My point with this illustration is that if your theory can not predict the past, it can’t predict the future. At least not robustly. Liberal people will always be with us. So will shy people. And atheists too. They may wax and wane, but human variation persists. On the evolutionary genetic level I think frequency dependent dynamics are such that the fait, in the medium term, of low fitness traits is generally to become oddballs, not extinct. And once they are odd they may become fortunes favorites….

* For real, is that his real name?

Democracy leads to Islamism

Filed under: Illiberalism,International Affairs,Islam — Razib Khan @ 12:36 am

The New York Times has a piece up on the rise in Islamic extremism in the Maldives, Maldives, Tourist Haven,
Casts Wary Eye on Growing Islamic Radicalism
. I want to highlight one section:

It was governed as a moderate Islamic nation for three decades under the autocratic rule of the former president, Maumoon Abdul Gayoom. But after the country made a transition to democracy in 2008, space opened up for greater religious expression, and conservative ideologies like Salafism cropped up.

Years ago in graduate school I told a friend that democracy and even economic prosperity did not monotonically lead to greater liberalism. In the long run perhaps, but in the short run it doesn’t necessarily do that at all.

Today we generally focus on the Islamic world, but there are plenty of examples in the past and in other places which suggest to us democratic populist passions can be quite illiberal. The Gordon Riots in England in the 18th century are a case where a pragmatic shift toward liberalism in regards to religious freedom for Roman Catholics triggered a Protestant populist riot. In the United States the emergence of universal white man’s suffrage during the Age of Jackson signaled the rise of a much more muscular and exclusive white supremacy in this country. In Iron Kingdom: The Rise and Downfall of Prussia, 1600-1947 you see the arc of democratization tethering itself to conservative rural vote-banks which reinforce aristocratic privilege. Finally, democratic developments in Burma have seen an associated increase in Buddhist radicalism.

Eric Kauffman argues in Shall the Religious Inherit the Earth? that modernization, economic development, and the expansion of political representation, integrates conservative rural populations and uplifts them all the while transforming the norms of urban areas. In other words, the rural bazar melds with the urban shopping mall, and both are changed. The 1979 revolution in Iran and its aftermath has been argued to be a victory of the bazar over the Western oriented gentry. In India the rise of Hindu nationalism is an assertion of the self-confidence of sub-elites from the “cow belt” who arose to challenge the Western oriented ruling class that had dominated since the early 20th century.

When the Arab Spring was in full swing in 2011 I wrote An Illiberal People:

In newly democratic nations which are pushed toward universal suffrage and the full panoply of democratic institutions the organic process of developing some safeguards for minorities and liberal norms has never evolved, because there was no evolution. Rather, these democracies are being created out of a box. Instead of a gradual shift toward more cultural conservatism with broader franchise, in these contexts it is a foundational aspect of the democratic system. I suspect this may have long term repercussions, as in other contexts liberal elites often institutionalized or established norms which served to check majoritarian populist impulses as they ceded much of their power over time.

The modern Left has a very anodyne view of Islam. It denies that there is something structurally within many Islamic societies which enables their illiberalism, the religion of Islam. In Islamic Exceptionalism Shadi Hamid argues that the religion itself may in some fundamental manner be inimical to the sort of secular liberal democratic society we perceive to be the terminal state of all cultures. I disagree with this view. Rather, I see in contemporary Islam the torture that Reformation era Christianity experienced attempting to navigate between an ideal of a universal church and the nascent emergence of nation-states. But in the short term both Shadi and I have the same prediction: greater democracy may lead to greater illiberalism and more repression of minorities. This an inconvenient truth for many Americans. But it may be true nonetheless.

June 19, 2017

Indian genetics, the never-ending argument

Filed under: Genetics,India,Indian Genetics,Indo-Europeans,science — Razib Khan @ 10:44 pm

I am at this point somewhat fatigued by Indian population genetics. The real results are going to be ancient DNA, and I’m waiting on that. But people keep asking me about an article in Swarajya, Genetics Might Be Settling The Aryan Migration Debate, But Not How Left-Liberals Believe.

First, the article attacks me as being racist. This is not true. The reality is that the people who attack me on the Left would probably attack magazines like Swarajya as highly “problematic” and “Islamophobic.” They would label Hindu nationalism as a Nazi derivative ideology. People should be careful the sort of allies they make, if you dance with snakes they will bite you in the end. Much of the media lies about me, and the Left constantly attacks me. I’m OK with that because I do believe that the day will come with all the ledgers will be balanced. The Far Left is an enemy of civilization of all stripes. I welcome being labeled an enemy of barbarians. My small readership, which is of diverse ideologies and professions, is aware of who I am and what I am, and that is sufficient. Either truth or power will be the ultimate arbiter of justice.

With that out of the way, there this one thing about the piece that I think is important to highlight:

To my surprise, it turned out that that Joseph had contacted Chaubey and sought his opinion for his article. Chaubey further told me he was shocked by the drift of the article that appeared eventually, and was extremely disappointed at the spin Joseph had placed on his work, and that his opinions seemed to have been selectively omitted by Joseph – a fact he let Joseph know immediately after the article was published, but to no avail.

Indeed, this itself would suggest there are very eminent geneticists who do not regard it as settled that the R1a may have entered the subcontinent from outside. Chaubey himself is one such, and is not very pleased that Joseph has not accurately presented the divergent views of scholars on the question, choosing, instead to present it as done and dusted.

I do wish Tony Joseph had quoted Gyaneshwer Chaubey’s response, and I’d like to know his opinions. Science benefits from skepticism. Unfortunately though the equivocation of science is not optimal for journalism, so oftentimes things are presented in a more stark and clear manner than perhaps is warranted. I’ve been in this position myself, when journalists are just looking for a quote that aligns with their own views. It’s frustrating.

There are many aspects of the Swarajya piece I could point out as somewhat weak. For example:

The genetic data at present resolution shows that the R1a branch present in India is a cousin clade of branches present in Europe, Central Asia, Middle East and the Caucasus; it had a common ancestry with these regions which is more than 6000 years old, but to argue that the Indian R1a branch has resulted from a migration from Central Asia, it should be derived from the Central Asian branch, which is not the case, as Chaubey pointed out.

The Srubna culture, the Scythians, and the people of the Altai today, all bear the “Indian” branch of R1a. First, these substantially post-date 6000 years ago. I think that that is likely due to the fact that South Asian R1a1a-Z93 and that of the Sbruna descend from a common ancestor. But in any case, the nature of the phylogeny of Z93 indicates rapid expansion and very little phylogenetic distance between the branches. Something happened 4-5,000 years ago. One could imagine simultaneous expansions in India and Central Asia/Eastern Europe. Or, one could imagine an expansion from a common ancestor around that time. The latter seems more parsimonious.

Additionally, while South Asians share ancestry with people in West Asia and Eastern Europe, these groups do not have distinctive South Asian (Ancestral South Indian) ancestry. This should weight out probabilities as to the direction of migration.

Second, I read some of the papers linked to in the article, such as Shared and Unique Components of Human Population Structure and Genome-Wide Signals of Positive Selection in South Asia and Y-chromosomal sequences of diverse Indian populations and the ancestry of the Andamanese. The first paper has good data, but I’ve always been confused by the interpretations. For example:

A few studies on mtDNA and Y-chromosome variation have interpreted their results in favor of the hypothesis,70–72 whereas others have found no genetic evidence to support it.3,6,73,74 However, any nonmarginal migration from Central Asia to South Asia should have also introduced readily apparent signals of East Asian ancestry into India (see Figure 2B). Because this ancestry component is absent from the region, we have to conclude that if such a dispersal event nevertheless took place, it occurred before the East Asian ancestry component reached Central Asia. The demographic history of Central Asia is, however, complex, and although it has been shown that demic diffusion coupled with influx of Turkic speakers during historical times has shaped the genetic makeup of Uzbeks75 (see also the double share of k7 yellow component in Uzbeks as compared to Turkmens and Tajiks in Figure 2B), it is not clear what was the extent of East Asian ancestry in Central Asian populations prior to these events.

Actually the historical and ancient DNA evidence both point to the fact that East Asian ancestry arrived in the last two thousand years. The spread of the first Gokturk Empire, and then the documented shift in the centuries around 1000 A.D. from Iranian to Turkic in what was Turan, signals the shift toward an East Asian genetic influx. Alexander the Great and other Greeks ventured into Central Asia. The people were described as Iranian looking (when Europeans encountered Turkic people like Khazars they did note their distinctive physical appearance).

We have ancient DNA from the Altai, and those individuals initially seemed overwhelmingly West Eurasian. Now that we have Scythian ancient DNA we see that they mixed with East Asians only on the far east of their range.

The second paper is very confused (or confusing):

The time divergence between Indian and European Y-chromosomes, based on the closest neighbour analysis, shows two different distinctive divergence times for J2 and R1a, suggesting that the European ancestry in India is much older (>10 kya) than what would be expected from a recent migration of Indo-European populations into India (~4 to 5 kya). Also the proportions suggest the effect might be less strong than generally assumed for the Indo-European migration. Interestingly, the ANI ancestry was recently suggested to be a mix of ancestries from early farmers of western Iran and people of the Bronze Age Eurasian steppe (Lazaridis et al. 2016). Our results agree with this suggestion. In addition, we also show that the divergence time of this ancestry is different, suggesting a different time to enter India.

Lazaridis et al. accept a mass migration from the steppe. In fact, the migration is to such a magnitude that I’m even skeptical. Also, there couldn’t have been a European migration to South Asia during the Pleistocene because Europeans as we understand them genetically did not exist then!!!

I assume that many of the dates of coalescence are sensitive to parameter conditions. Additionally, they admit limitations to their sampling.

Ultimately the final story will be more complex than we can imagine. R1a is too widespread to be explained by a simple Indo-Aryan migration in my opinion. But we can’t get to these genuine conundrums if we keep having to rebut ideologically motivated salvos.

Related: Ancient herders from the Pontic-Caspian steppe crashed into India: no ifs or buts. I wish David would be a touch more equivocal. But I have to admit, if the model fits, at some point you have to quit.

June 18, 2017

Open Thread, 06/18/2017

Filed under: Open Thread — Razib Khan @ 9:38 pm

In the centuries around and before 1000 A.D. there was a “Viking international” of sorts. Harald Hardrada may have died in England trying to become king of that nation, but he served for a time in the Varangian Guards in Constantinople. His connections to Kievan Rus were such that priests in the Eastern Christian tradition were brought in to aid in the conversion of Norway. The book The Vikings talks about much of this.

Speaking of Kievan Rus, as I noted in the comments below the Y chromosomal lineage of the Rurikids is clearly one of Finns, not Scandinavians. But the Primary Chronicle indicates that the recent ancestors of Vladimir the Great were Scandinavian, so the cultural assimilation must have occurred earlier.

And Kievan Rus itself was more connected to other parts of Europe than Russia itself later would be. Anne of Kiev was the mother of a future king of France

An Expanded View of Complex Traits: From Polygenic to Omnigenic. Everyone is talking about this. Have not read it. A lot of the discussion is going on on Twitter. Jonathan Pritchard has been very active in the discussions.

Punctuated evolution shaped modern vertebrate diversity. This paper is about morphology, but still cool.

How genetics is settling the Aryan migration debate. The author follows me on Twitter and quotes me in the piece (from one of my blog posts in 2009). He clearly knows his stuff and seems to have read my posts, so nothing new. But he does get some scientists to put into the record that they don’t believe things they believed in the late 2000s. One problem is that Indian “Out of India” proponents keep citing papers from the late 2000s which the authors themselves likely don’t stand by anymore.

Reading a bit of A Cooperative Species: Human Reciprocity and Its Evolution. I feel the field of human behavioral ecology gets short shrift, though to be fair before Joe Heinrich started writing books there really weren’t any popularizers (both David Sloan Wilson and E. O. Wilson do do some on the side in this area).

Berkeley Says It’s Standing Up to Trump, But It’s Actually Busy Arguing About Zucchini. Median home price in Berkeley is now $1,100,000.

Over the past year for various reasons I’ve gained 10 pounds. My waste has gone from 29-30 inches to 31-32. They did a measurement at the gym and my body fat is now 17%.

So I’m going on a ketogenic diet to cut some of the fat. Any advice is welcome.

The Finnic peoples emerged in Baltic after the Bronze Age

Filed under: Finland,History — Razib Khan @ 10:07 am


A reader in the comments reminds me there has been a preprint which is relevant to the population structure of Baltic Europe which came out a few months ago, Extensive farming in Estonia started through a sex-biased migration from the Steppe:

…Here we present the analyses of low coverage whole genome sequence data from five hunter-gatherers and five farmers of Estonia dated to 4,500 to 6,300 years before present. We find evidence of significant differences between the two groups in the composition of autosomal as well as mtDNA, X and Y chromosome ancestries. We find that Estonian hunter-gatherers of Comb Ceramic Culture are closest to Eastern hunter-gatherers. The Estonian first farmers of Corded Ware Culture show high similarity in their autosomes with Steppe Belt Late Neolithic/Bronze Age individuals, Caucasus hunter-gatherers and Iranian farmers while their X chromosomes are most closely related with the European Early Farmers of Anatolian descent…

As you can see in the PCA plot above the Comb Ceramic Culture and the Corded Ware culture in Estonia are modeled well by the three ancestral populations hypothesis for Europe. The problem with this is that Finns and Russians with Finnic background do not fit with this model. There has been clear later gene flow.

From the text:

Interestingly, modern Estonians showed a bigger proportion of the blue component [associated with European hunter-gatherers] than CWC individuals. Comparing to CCC individuals, modern Estonians lack the red component [Eastern Siberian]. This, together with the absence of Y chromosome hg N in CCC and CWC, points to further influx and change of genetic material after the arrival of CWC.

The sample sizes are small. Additionally these are from Estonia, not Finland. But the Comb Ceramic Culture was widespread throughout the region.

Also, from a 2015 paper (supplements):

Among the northern Europeans, the Finnish (finni3) show evidence of an admixture event involving a minority source most similar to contemporary North Siberians (469CE (213BCE-1011CE)). Finns are thought to have originated from the northward migration, and subsequent contact, between Central Europeans and indigenous Scandinavian hunter-gatherers closely related to the Saami [S33]. The Saami are closely related to the individuals that make up the North Siberian world region, and whilst our confidence in this admixture date is low because of the small size of the cluster, the event we see is likely to represent this key period in Finnish history.

The “North Siberia” cluster are: Selkup, Chukchi, Dolgan, Ket, Koryak, Nganassan, Yakut and Yukagir. The admixture is very recent. I suspect too recent. But it gets us to the qualitative point that the Siberian admixture into Finns is probably not that old.

Related: The Origin of the Finnic Peoples.

June 17, 2017

The origin of the Finnic peoples

Filed under: Finland,History — Razib Khan @ 8:13 pm

 

One of the very first things I wrote about in relation to historical population genetics was in on the origins of the Finnic peoples. The reasons are two fold:

– first, the Finns and Estonians speak language is rather peculiar in a Europe dominated by Indo-European tongues (I suspect one reason that Tolkien based Quenya, the high elvish language, on Finnish is that it is so otherworldy to the Germanic ear. The Sindarin language, which was the common tongue of elves in Middle Earth, was based on Welsh). Rather, the distribution to the Uralic languages extends to the east, as far as Siberia. Even the closest affinities to Finnish and Estonian extend eastward, as there are Karelians who live deep in northwest Russia.

– second, there were peculiarities in the genetics of the Finns which date back to the 20th century that have always been notable.

Some of the distinctiveness of the Finns clearly has to do with the demographic isolation of the recent past, and the range expansion into the north and east. I will ignore this aspect of recent drift, and focus on their deep history and phylogenetic relationships.

New molecular genetic techniques in the 1980s and 1990s which enabled the genotyping of Y and mtDNA lineages immediately yielded the fact that the paternal heritage of the Finns is very unique in comparison to their neighbors, and erstwhile hegemons, the Scandinavians. While Swedes tend to be haplogroup I (indigenous to Western Europe dating to the late Pleistocene) or one of the two R1 lineages (intrusive from the Eurasian steppe during the Bronze Age), Finns tend to be haplogroup N3, with a substantial minority of I. While 63 percent of Finns are N3, only 3 percent of Swedens are. Due through the reality of migration of Finns to Sweden, as well as the prevalence of Saami all across Northern Sweden until the early modern period, Swedish N3 may be due to gene flow in the last thousand years. The two R1 lineages are ~10% of the Finnish paternal gene pool, they’re strongly skewed toward R1a, while the ~40% of Swedish R1 lineages are balanced.

In contrast the mtDNA profiles of Finns are very similar to their neighbors. Like Sweden the dominant haplogroup is a branch of H, with the reduced fraction accountable for the fact that Finns have a higher percentage of U5, which has been associated with European hunter-gatherers. The various haplogroups (e.g., T) associated with Early European Farmers are at somewhat lower frequency in Finland than Sweden.

A simple explanation then presents itself to us: the Finns have been subjected to male mediated admixture into a “conventional” European substrate. But there has been long been controversy as to whether the Finnish N3 haplogroup was indigenous to Europe, or its presence in Northeast Europe was due to migration. If it was indigenous than the admixture model does not make as much sense. But as with many things we’ve moved very far in comparison to where we were when I first began to look at this issue in 2002.

If you read Human Y Chromosome Haplogroup N: A Non-trivial Time-Resolved Phylogeography that Cuts across Language Families the likelihood than the Y chromsomal structure of Finland is old seems low. First, Finnish N3 lineages are very young and underwent rapid expansion beginning 4 to 6 thousand years ago (this is evident in their whole genome variation pattern). Second, the most diversity of N seems to be in Western Siberia. Third, N exists in higher frequencies in parts of Siberia than even in Finland. Fourth, the range of N pushes it all the way to the Pacific Ocean. It is not implausible that it expanded from one rim of Eurasia to the other, but the most likely scenario is that it came from somewhere in the middle.

Also, it is likely that there has been admixture into Finns from an East Eurasian population. To give some examples, a derived SNP at EDAR is at very high frequency in Northeast Asians. The ancestral variant is dominant outside of East Asia and the New World. In Europe among modern Europeans the derived variant of EDAR is not present in indigenous populations. A quick check in the 10000 Genomes data shows that it’s at ~6% in Finns (in contrast, the ancestral variant of SLC24A5 is present at frequencies of ~1; this could be random, but I suspect in situ selection….). You can see that the derived variant is absent in a rather large sampling of other Europeans.

Running ADMIXTURE unsupervised it’s immediately obvious that Finnic peoples have a minority component of East Eurasian admixture. This dark blue element is absent in most of the Swedes. Not surprisingly the Russians exhibit structure depending on where you sample. Some Russian populations are clearly Slavicized relatively recently, and exhibit a genetic profile rather like Finnic peoples (this northern Russian regions also have high frequencies of haplogroup N, which is much rarer in the south or among Ukrainians).

There’s a cline that runs east to west in relation to this component. The Finn’s neighbors immediately to the east, Karelians and Veps, have a higher fraction than the Finns proper. Additionally, some Finns in the data seem to lack it totally. One might speculate that these are people of Swedish origin who eventually assimilated to the Finnish identity. This is not impossible. In the 19th century Finnish nationalism was sparked in large part by middle class activists, many of whom were Swedish ethno-linguistically due to the connections between class and language at that time. But these individuals may be evidence of older structure in Finland. More on that later.

I also ran some Treemix on a subset of the data. You see there is gene flow coming into the Finns from a Siberian group. I used Nenets (a group of Samoyeds) and Yakut because the former have more linguistically in common with the Finns, while the latter are used by companies like 23andMe (Yakuts are the most northeasterly Turkic people). Strangely the Karelians and Veps get gene flow from Nenets, while the Finns get it from Yakuts (I pruned with PCA and ADMIXTURE to remove individuals with recent European ancestry).

But the model of a single pulse admixture is probably wrong anyhow. Rather, the spread of Finnic hunters and gatherers may have gradual, and/or occurred in several pulses. On the fringe of Northern Eurasia local extinctions were probably common. The landscape of Northern Eurasia, from the Baltic to Siberia, may long have been rather dynamic, with interactions between Uralic, Indo-European and Altaic peoples.

At this point I am at a loss. The archaeology of Finland is not something I know well, and the academic literature is hard for me to track down. Some scholars believe that the Comb Ceramic Culture plays a major role in the ethnogenesis of the people we call Finns. During the Bronze Age the Corded Ware zone spread into southern Finland, bringing agriculture. The fusion between the Comb Ceramic and Corded Ware led up to the societies which are first mentioned by Classical authors.

Finland was always liminal to early agriculture, and the Corded Ware Indo-Europeans may eventually have given away to the forest Finns as the climate turned more difficult. The predominance of N3 haplogroups may be a function of the nature of patriarchal societies, where certain lineages maintain powerful long term advantages.

Indian media is finally reporting on the Aryan migration into South Asia

Filed under: Genetics,science — Razib Khan @ 2:49 pm

For various ideological reasons in India there has been a strong resistance to the idea that Aryans came from outside of South Asia. When David Reich’s Reconstructing Indian Population History was published 2009 the Indian media had a weird response. For example, Aryan-Dravidian divide a myth: Study.

Though Reich’s paper was equivocal, it was clear to me that it was likely going to be the launching point for a resurrection of the Aryan migration theory. Now Tony Joseph in The Hindu has published a pretty good survey of the literature, How genetics is settling the Aryan migration debate. Nothing new for readers of this weblog, but he some good quotes:

The avalanche of new data has been so overwhelming that many scientists who were either sceptical or neutral about significant Bronze Age migrations into India have changed their opinions. Dr. Underhill himself is one of them. In a 2010 paper, for example, he had written that there was evidence “against substantial patrilineal gene flow from East Europe to Asia, including to India” in the last five or six millennia. Today, Dr. Underhill says there is no comparison between the kind of data available in 2010 and now. “Then, it was like looking into a darkened room from the outside through a keyhole with a little torch in hand; you could see some corners but not all, and not the whole picture. With whole genome sequencing, we can now see nearly the entire room, in clearer light.”

In relation to online debates I have had Indian interlocutors tell me flat out that they believe in the papers published between 2005 and 2010. It is nice to get the scientists who actually published this work now admit that new results overturn the older theories.

Note: I am going to refer to this as a migration, because “invasion” seems to connote too much specificity as to how it happened. But I have a difficult time imagining that it was a peaceful process.

Amazon purchases whole foods and the distribution channel comes to you

Filed under: Amazon,Economics,Whole Foods — Razib Khan @ 8:07 am

The purchase of Whole Foods by Amazon has sent grocery store stocks into tailspin. Could Amazon do to Safeway and Korger what it did to Borders and Barnes & Noble?

Some people have observed that the purchase impacts the nascent grocery delivery sector more than the established supermarkets. That was my first thought. For me Saturday used to involve a trip to Whole Foods. But not anymore. Basically I use Instacart. (I can’t use Amazon Fresh because it doesn’t delivery to where I live. For now….)

Because Amazon is such a monster of a company people are talking about grocery stores as the underdog in this new war. But the reality is that what we think of “grocery store” is something far different from what someone in 1900 would have imagined. Americans today assume that the supermarket is synonymous with groceries. But supermarkets as institutions are economic innovations which date to the 20th century. The rise of the sector by showcasing its pioneering firm is detailed in The Great A&P and the Struggle for Small Business in America. As the title makes clear the rise of supermarkets resulted in a massive creative destruction in the American economy and culture.

Before A&P reimagined the profession being a grocer was a way for working class men to have a job that could support a family and give them some independence. But as the supermarkets cannibalized small grocers, men who had run their own businesses became employees in large corporations. Entrepreneurs became clerks. Creative destruction also worked so that eventually A&P was marginalized by new-model supermarkets that catered to suburban families. Today Walmart and Whole Foods have been attacking the low and top ends of the market and squeezing out smaller players.

Walmart’s battle from the bottom-up seems to have beaten Whole Foods’ premium strategy. Amazon’s purchase makes sense since Whole Foods has some assets major it can bring to the battle, but Walmart scale just too much for them to tackle.

As we all know the retail sector is changing. Half of millennials now buy groceries online at least some of the time. Malls are closing as their anchor department stores struggle. Where would a modern day Tiffany do her tour? Obviously it’s YouTube.

But that doesn’t mean that people won’t venture out. Upscale retail plazas are replacing the role of malls. Independent bookstores are still around, while Borders is gone and Barnes & Noble is a shadow of what it was. The positive aspect of the death of bricks and mortar retail is that we spend less time out and about on errands. Rather, we go out to eat at a restaurant, or meet friends in the park or at a bar. The downside is a smaller and smaller set of firms are dominating the supply chains between producers and consumers. I think Amazon will be targeted by antitrust considerations in the 2020s.

June 16, 2017

The cultural revolution that will happen in China

Filed under: Baby Sequencing,DTC personal genomics,Veritas — Razib Khan @ 6:02 pm

If you’ve been hiding under a rock, please see Baby Genome Sequencing for Sale in China:

A Boston-based DNA sequencing company is offering to decode the complete genomes of newborns in China, leading some to ask how much parents should know about their children’s genes at birth.

Veritas Genetics says the test, ordered by a doctor, will report back on 950 serious early- and later-life disease risks, 200 genes connected to drug reactions, and more than 100 physical traits a child is likely to have.

Called myBabyGenome, the service costs $1,500 and could help identify serious hidden problems in newborns, the company says.

Obviously a $1,500 price point is beyond most Chinese. But the total fertility rate in China today is 1.56, and almost certainly lower among urban elites who could actually afford this service. Considering that genome is will you for life, more or less, $1,500 isn’t really that much.

For years there have been many fly by night genetics companies who have some presence in East Asia. They come and go. The combination of a lax regulatory environment and the allure of “genes” means that there is some money to be made. Veritas in contrast is a serious company. This is heralding the reality that widespread sequencing is going to go primetime.

Of course there is skepticism. Fortunately the piece doesn’t talk much to people who who express Leon Kass style FUD. The objections are scientific:

But some doctors say the plan is a huge overstep. “I think it’s vastly premature to peddle a completely unproven set of data, especially to a vulnerable population like neonates,” says Jim Evans, a professor of genetics at the University of North Carolina Chapel Hill.

The problem is that the risk posed by many disease genes remains uncertain. Even if a child has a mutation in a gene, he or she may never be affected, prompting debate among doctors about whether it’s useful to inform parents.

These are real objections, but I don’t see why sequencing should not be allowed as a choice by parents nevertheless. And widespread adoption of sequencing would actually allow us to start obtaining more data that we could use to make better decisions in the future. The genomics space for a while has had a bit of a chicken & egg problem. The sequencing is starting to get there, but we still need to get phenotypes. And this seems like one way to get the public involved and feel like they have a stake.

Like in vitro fertilization I see neonatal sequencing as inevitable in regards to whether it will be ubiquitous. It will be common. And “ethical problems” won’t really come up in the future because people will be comfortable with it. Right now there’s a fear factor.

This is in sharp contrast with CRISPR. That’s a technology that will have real consequences, and like male circumcision may be difficult to reverse for someone who as an adult was modified in infancy. In contrast a genome sequence is just more information.

For years may people have speculated that genetic testing technology will really begin to take off in Asia because for various reasons Americans and Europeans are wary. To me this is a signal that that might be occurring, depending on how successful Veritas’ venture is.

This is perhaps the most important point:
But Veritas will not reveal everything, in recognition that not all the information in the genome is appropriate to give parents right away. For instance, it won’t tell them about a gene that can strongly predispose people to Alzheimer’s in old age.

Instead, Veritas says, it will retain the rest of a newborn’s genome data and let parents purchase further information at a later date.

I think this may be more common than we think. Most people don’t want to deal with a ~3 GB text file. That being said, I think they should in the future have an option for people to buy their data outright.

Addendum: I met Robert Green at SxSW. Nice fellow. One thing that he mentioned was widespread opposition among physicians. I suspect one dynamic that MDs won’t like in the near future is decentralization of the distribution of medical services away from their own profession. This is part of it.

June 15, 2017

The system of the world by William H. McNeill

Filed under: History — Razib Khan @ 9:13 pm

In the post below on book recommendations I forgot to mention William H. McNeill and John Robert McNeill’s The Human Web: A Bird’s-Eye View of World History. It’s arguably been one of the most influential works that has percolated in my mind throughout the years. It’s less than 400 pages, and illustrates in broad sketches that history has been through many random shocks, but that there are broad patterns that one can discern.

The elder McNeill is most famous for The Rise of the West and Plagues and Peoples. To a great extent he was Jared Diamond before there ever was Jared Diamond.

Unfortunately I did not notice that McNeill died last summer. From his obituary:

Refuting Francis Fukuyama’s premise in “The End of History and the Last Man” in 1992 that the American model of a liberal, capitalist democracy had become the paradigm for governance, Professor McNeill wrote in The New York Times Book Review: “I do not believe that human nature is uniform and unchanging. Rather, whatever penchants and capabilities we inherit with our genes are so malleable that their expression takes infinitely diverse forms.”

“When Asian models of social and economic efficiency seem to be gaining ground every day, and when millions of Muslims are at pains to sustain the differences, great and small, that distinguish them from Americans,” he continued, “it is hard to believe that all the world is destined to imitate us.”

June 14, 2017

The fad for dietary adaptations is not going away

Filed under: Diet,FADS,Genetics,Human Genetics — Razib Khan @ 7:21 pm


Food is a big deal for humans. Without it we die. Unlike some animals (here’s looking at you pandas) we’re omnivorous. We eat fruit, nuts, greens, meat, fish, and even fungus. Some of us even eat things which give off signals of being dangerous or unpalatable, whether it be hot sauce or lutefisk.

This ability to eat a wide variety of items is a human talent. Those who have put their cats on vegetarian diets know this. After a million or so years of being hunters and gatherers with a presumably varied diet for thousands and thousands of years most humans at any given time ate some form of grain based gruel. Though I am sympathetic to the argument that in terms of quality of life this was a detriment to median human well being, agriculture allowed our species to extract orders of magnitude more calories from a unit of land, though there were exceptions, such as in marine environments (more on this later).

Ergo, some scholars, most prominently Peter Bellwood, have argued that farming did not spread through cultural diffusion. Rather, farmers simply reproduced at much higher rates because of the efficiency of their lifestyle in comparison to that of hunter-gatherers. The latest research, using ancient DNA, broadly confirms this hypothesis. More precisely, it seems that cultural revolutions in the Holocene have shaped most of the genetic variation we see around us.

But genetic variation is not just a matter of genealogy. That is, the pattern of relationships, ancestor to descendent, and the extent of admixtures across lineages. Selection is also another parameter in evolutionary genetics. This can even have genome-wide impacts. It seems quite possible that current levels of Neanderthal ancestry are lower than might otherwise have been the case due to selection against functional variants derived from Neanderthals, which are less fitness against a modern human genetic background.

The importance of selection has long been known and explored. Sickle-cell anemia only exists because of balancing selection. Ancient DNA has revealed that many of the salient traits we associate with a given population, e.g., lactose tolerance or blue eyes, have undergone massive changes in population wide frequency over the last 10,000 years. Some of this is due to population replacement or admixture. But some of it is due to selection after the demographic events. To give a concrete example, the frequency of variants associated with blue eyes in modern Europeans dropped rapidly with the expansion of farmers from the Near East ~10,000 years ago, but has gradually increased over time until it is the modal allele in much of Northern Europe. Lactase persistence in contrast is not an ancient characteristic which has had its ups and downs, but something new that evolved due to the cultural shock of the adoption of dairy consumption by humans as adults. The region around lactase is one of the strongest signals of natural selection in the European genome, and ancient DNA confirms that the ubiquity of the lactase persistent allele is a very recent phenomenon.

But obviously lactase is not going to be the only target of selection in the human genome. Not only can humans eat many different things, but we change our portfolio of proportions rather quickly. In a Farewell to Alms the economic historian Gregory Clark observed that English peasants ate very differently before and after the Black Death. As any ecologist knows populations are resource constrained when they are near the carrying capacity, and England during the High Medieval period there was massive population growth due to gains in productivity (e.g., the moldboard plough) as well as intensification of farming and utilization of all the marginal land.

After the Black Death (which came in waves repeatedly) there was a massive population decline across much of Europe. Because institutions and practices were optimized toward maintaining a much higher population, European peasants lived a much better lifestyle after the population crash because the pie was being cut into far fewer pieces. In other words, centuries of life on the margins just scraping by did not mean that English peasants couldn’t live large when the times allowed for it. We were somewhat pre-adapted.

Our ability to eat a variety of items, and the constant varying of the proportions and kind of elements which go into our diet, mean that sciences like nutrition are very difficult. And, it also means that attempts to construct simple stories of adaptation and functional patterns from regions of the genome implicated in diet often fail. But with better analytic technologies (whole genome sequencing, large sample sizes) and some elbow grease some scientists are starting to get a better understanding.

A group of researchers at Cornell has been taking a closer look at the FADS genes over the past few years (as well as others at CTEG). These are three nearby genes, FADS1FADS2, and FADS3 (they probably underwent duplication). These genes are involved in the metabolization of fatty acids, and dietary regime turns out to have a major impact on variation around these loci.

The most recent paper out of the Cornell group, Dietary adaptation of FADS genes in Europe varied across time and geography:

Fatty acid desaturase (FADS) genes encode rate-limiting enzymes for the biosynthesis of omega-6 and omega-3 long-chain polyunsaturated fatty acids (LCPUFAs). This biosynthesis is essential for individuals subsisting on LCPUFA-poor diets (for example, plant-based). Positive selection on FADS genes has been reported in multiple populations, but its cause and pattern in Europeans remain unknown. Here we demonstrate, using ancient and modern DNA, that positive selection acted on the same FADS variants both before and after the advent of farming in Europe, but on opposite (that is, alternative) alleles. Recent selection in farmers also varied geographically, with the strongest signal in southern Europe. These varying selection patterns concur with anthropological evidence of varying diets, and with the association of farming-adaptive alleles with higher FADS1 expression and thus enhanced LCPUFA biosynthesis. Genome-wide association studies reveal that farming-adaptive alleles not only increase LCPUFAs, but also affect other lipid levels and protect against several inflammatory diseases.

The paper itself can be difficult to follow because they’re juggling many things in the air. First, they’re not just looking at variants (e.g., SNPs, indels, etc.), but also the haplotypes that the variants are embedded in. That is, the sequence of markers which define an association of variants which indicate descent from common genealogical ancestors. Because recombination can break apart associations one has to engage with care in historical reconstruction of the arc of selection due to a causal variant embedded in different haplotypes.

But the great thing about this paper is that in the case of Europe they can access ancient DNA. So they perform inferences utilizing whole genomes from many extant human populations, but also inspect change in allele frequency trajectories over time because of the density of the temporal transect. The figure to the left shows variants in both an empirical and modeling framework, and how they change in frequency over time.

In short, variants associated with higher LCPUFA synthesis actually decreased over time in Pleistocene Europe. This is similar to the dynamic you see in the Greenland Inuit. With the arrival of farmers the dynamic changes. Some of this is due to admixture/replacement, but some of it can not be accounted for admixture and replacement. In other words, there was selection for the variants which synthesize more LCPUFA.

This is not just limited to Europe. The authors refer to other publications which show that the frequency of alleles associated with LCPUFA production are high in places like South Asia, notable for a culture of preference for plant-based diets, as well as enforced by the reality that animal protein was in very short supply. In Europe they can look at ancient DNA because we have it, but the lesson here is probably general: alternative allelic variants are being whipsawed in frequency by protean shifts in human cultural modes of production.

In War Before Civilization Lawrence Keeley observed that after the arrival of agriculture in Northern Europe in a broad zone to the northwest of the continent, facing the Atlantic and North Sea, farming halted rather abruptly for centuries. Keeley then recounts evidence of organized conflict in between two populations across a “no man’s land.”

But why didn’t the farmers just roll over the old populations as they had elsewhere? Probably because they couldn’t. It is well known that marine regions can often support very high densities of humans engaged in a gathering lifestyle. Though not farmers, these peoples are often also not nomadic, and occupy areas as high density. The tribes of the Pacific Northwest, dependent upon salmon fisheries, are classic examples. Even today much of the Northern European maritime fringe relies on the sea. High density means they had enough numbers to resist the human wave of advance of farmers. At least for a time.

Just as cultural forms wane and wax, so do some of the underlying genetic variants. If you dig into the guts of this paper you see much of the variation dates to the out of Africa period. There were no great sweeps which expunged all variation (at least in general). Rather, just as our omnivorous tastes are protean and changeable, so the genetic variation changes over time and space in a difficult to reduce manner. The flux of lifestyle change is probably usually faster than biological evolution can respond, so variation reducing optimization can never complete its work.

The modern age of the study of natural selection in the human genome began around when A Map of Recent Positive Selection In the Human Genome was published. And it continues with methods like SDS, which indicate that selection operates to this day. Not a great surprise, but solidifying our intuitions. In the supplements to the above paper the authors indicate that the focal alleles that they are interrogating exhibit coefficients of selection around ~0.5% or so. This is rather appreciable. The fact that fixation has not occurred indicates in part that selection has reversed or halted, as they noted. But another aspect is that there are correlated responses; the FADS genes are implicated in many things, as the authors note in relation to inflammatory diseases. But I’m not sure that the selection effects of these are really large in any case. I bet there are more important things going on that we haven’t discovered or understood.

Obviously genome-wide analyses are going to continue for the foreseeable future. Ten years ago my late friend Mike McKweon predicted that at some point genomics was going to have be complemented by detailed follow up through bench-work. I’m not sure if we’re there yet, but there are only so many populations you can sequence, and only to a particular coverage to obtain any more information. Some selection sweeps will be simple stories with simple insights. But I suspect many more like FADS will be more complex, with the threads of the broader explanatory tapestry assembled publications by publication over time.

Citation: Ye, K., Gao, F., Wang, D., Bar-Yosef, O. & Keinan, A. Dietary adaptation of FADS genes in Europe varied across time and geography. Nat. Ecol. Evol. 1, 0167 (2017).

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