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May 21, 2018

The mutation accumulation controversy continues….

Filed under: Mutation,Population genetics — Razib Khan @ 10:56 pm

Every few years I check to see if the great mutation accumulation controversy has resolved itself. I don’t know if anyone calls it that, but that’s what I think of it as. There are two major issues that matter here: mutation rates are a critical parameter in evolutionary models, and, mutation accumulation over time matters for parental age effects when it comes to disease (speaking as an older father!).

In the latter case, I’m talking about the reasons that people freeze their eggs or sperm. In the former case, I’m talking about whether we can easily extrapolate mutation rates over evolutionary time as semi-fixed, so we can infer dates of last common ancestry and such. To give a concrete example of what I’m talking about, if mutation rates varied a lot over the evolutionary history of our hominin lineage, then we might need to rethink some of the inferred timings.

Today two preprints came out on mutation accumulation. First, Overlooked roles of DNA damage and maternal age in generating human germline mutations. Second, Reproductive longevity predicts mutation rates in primates. What a coincidence in synchronicity!

Additionally, the last author on the second preprint, Matt Hahn, is someone I’ll be doing a podcast with this week. So aside from talking about neutral theory, and his book Molecular Population Genetics, I’m going to have to bring up this mutation business.

The figure above from the first preprint shows that the proportion of mutations derived from the father don’t increase over time, as textbooks generally state. Why would we expect this? Sperm keeps replicating after puberty so you should be gaining more mutations. In contrast, the eggs are arrested in meiosis. There are various mechanistic reasons that the authors of the first preprint give for why the ratio does not change between paternal and maternal mutations (e.g., non-replicative mutations seem to be the primary one). The authors are using a very “pedigree” strategy, rather than an “evolutionary” one. They’re looking at sequenced trios, and noticing patterns. I think in the near future they’ll be far more sure of what’s going on because they’ll have bigger sample sizes. They admit the effects are subtle (also, some of the p-values are getting close to 0.05).

Instead of focusing on a human pedigree, the second preprint does some sequencing on owl monkeys (I had no idea there were “owl monkeys” before this paper). They find that the mutation rate is ~32% lower in owl monkeys than in humans. Why is this?

The plot to the left shows that mutations increase across age with species (though the number of data points is pretty small). The authors contend that:

The association between mutation rates and reproductive longevity implies that changes in life history traits rather than changes to the mutational machinery are responsible for the evolution of these rates. Species that have evolved greater reproductive longevity will have a higher mutation rate per generation without any underlying change to the replication, repair, or proofreading proteins.

If I read this right: owl monkeys reproduce fast and don’t have as much reproductive longevity. Ergo, lower mutation rates (less mutational build-up from paternal side).

After all these years I’m still not convinced about anything. I assume that eventually bigger data sets will come online and we’ll resolve this. Someone has to be right!

(not too many people on Twitter get what’s going on either)

May 20, 2018

Beyond “Out of Africa” within Africa

Filed under: Human Evolution,Population genomics,Uncategorized — Razib Khan @ 11:36 pm

It looks as if the vast majority (95% or more depending on the population) of the ancestry of non-African humans derives from a population expansion which began around ~60,000 years ago. Before this period some researchers argue there was a non-trivial period of isolation. The “long bottleneck” (David Reich alludes to this in Who We Are and How We Got Here: Ancient DNA and the New Science of the Human Past). For the vast majority of humans then the last 60,000 years is characterized by a branching process, some reticulation (e.g., South Asians merge West and East Eurasian lineages) between these branches from a common ancestor, as well as introgression from archaic lineages like Neanderthals and Denisovans.

Though I do accept that it seems that modern humans probably migrated out of Africa before 60,000 years ago, mostly due to the results from archaeology, I think the genetic evidence is strong that these groups contributed very little genetically to contemporary populations.

The situation within Africa is very different. Being conservative it seems likely that the Khoisan ancestral lineage diverged from some other Africans ~200,000 years ago. I say conservative because there are researchers who want to push the divergence much further back. Additionally, several different research groups are now converging in a result that West Africans are a mixture between eastern Sub-Saharan Africans (think the population ancestral to Mota in Ethiopia) and a lineage basal to all other humans. That means that the Khoisan are not the most basal, so even assuming the conservative 200,000 year divergence point for Khoisan, modern humans share a common ancestor earlier than 200,000 years ago.

The upshot here is that around 75 percent of the history of modern humans is within (greater)* Africa. The distinctive “Out of Africa” bottleneck and expansion defines most humans only in the last 25 percent of the history of our species. And, within Africa, the dynamics were very different. The biggest difference is that African populations are not defined by a large number of lineages emerging and diverging around the same period, because there wasn’t a massive and singular expansion within Africa analogous to what occurred outside of Africa (at least until the recent past, with the Bantu expansion). That’s why there’s deep structure within Africa today between groups as divergent as the Bantu, Mbuti, Hadza, and Khoisan.

The term “Basal Eurasian” kind of makes sense in the non-African context because of the singular importance of divergence between lineages in the first 10,000 years or so after the “Out of Africa” event. I’m not sure “Basal human” makes as much sense because there wasn’t a singular event within Africa that allowed for the emergence of modern humans. Rather, it was a process, and probably quite resembles something like multiregionalism.

* Some wiggle room here for the likelihood that modern humans were long present in the liminal Near East.

Beyond “Out of Africa” within Africa

Filed under: Human Evolution,Population genomics — Razib Khan @ 11:36 pm

It looks as if the vast majority (95% or more depending on the population) of the ancestry of non-African humans derives from a population expansion which began around ~60,000 years ago. Before this period some researchers argue there was a non-trivial period of isolation. The “long bottleneck” (David Reich alludes to this in Who We Are and How We Got Here: Ancient DNA and the New Science of the Human Past). For the vast majority of humans then the last 60,000 years is characterized by a branching process, some reticulation (e.g., South Asians merge West and East Eurasian lineages) between these branches from a common ancestor, as well as introgression from archaic lineages like Neanderthals and Denisovans.

Though I do accept that it seems that modern humans probably migrated out of Africa before 60,000 years ago, mostly due to the results from archaeology, I think the genetic evidence is strong that these groups contributed very little genetically to contemporary populations.

The situation within Africa is very different. Being conservative it seems likely that the Khoisan ancestral lineage diverged from some other Africans ~200,000 years ago. I say conservative because there are researchers who want to push the divergence much further back. Additionally, several different research groups are now converging in a result that West Africans are a mixture between eastern Sub-Saharan Africans (think the population ancestral to Mota in Ethiopia) and a lineage basal to all other humans. That means that the Khoisan are not the most basal, so even assuming the conservative 200,000 year divergence point for Khoisan, modern humans share a common ancestor earlier than 200,000 years ago.

The upshot here is that around 75 percent of the history of modern humans is within (greater)* Africa. The distinctive “Out of Africa” bottleneck and expansion defines most humans only in the last 25 percent of the history of our species. And, within Africa, the dynamics were very different. The biggest difference is that African populations are not defined by a large number of lineages emerging and diverging around the same period, because there wasn’t a massive and singular expansion within Africa analogous to what occurred outside of Africa (at least until the recent past, with the Bantu expansion). That’s why there’s deep structure within Africa today between groups as divergent as the Bantu, Mbuti, Hadza, and Khoisan.

The term “Basal Eurasian” kind of makes sense in the non-African context because of the singular importance of divergence between lineages in the first 10,000 years or so after the “Out of Africa” event. I’m not sure “Basal human” makes as much sense because there wasn’t a singular event within Africa that allowed for the emergence of modern humans. Rather, it was a process, and probably quite resembles something like multiregionalism.

* Some wiggle room here for the likelihood that modern humans were long present in the liminal Near East.

The end of the century of privacy

Filed under: Privacy,Urbanism,Urbanization — Razib Khan @ 10:40 pm

Reading The Rise and Fall of American Growth: The U.S. Standard of Living since the Civil War has made me think more about the unique nature of urban civilization of the long 20th-century. The expansion of public health, in particular provision of clean water, meant that for the first time in the history of the world you had a situation where people in cities actually had a higher life expectancy than those in rural areas. Prior to this cities were demographic sinks. We have data from the 19th century which makes it clear that morbidity was higher for city dwellers. This is probably the major reason, in my opinion, the cosmopolitan worlds of antiquity had such a marginal demographic impact: the culturally vibrant city-dwellers who dominated Classical civilization politically and socially didn’t leave many descendants.

Even though cities were dominant politically and central to many earlier societies, only in the last century so have predominantly urban societies emerged. Before that most humans lived in villages or in hunter-gatherer bands. Everyone was in everyone else’s business. Anonymity was simply not a thing for most humans in most periods of our species’ history.

This changed with the rise of cities. In the early 2000s the anthropologist Robin Dunbar argued that people could maintain ~150 genuine social relationships in their mind. This is Dunbar’s number. Over the past two decades, there have been lots of arguments about Dunbar’s number. One can stipulate that the value may not be 150. Additionally, it seems likely that some people have a higher Dunbar’s numbers than others. But the general point that human social competencies have a ceiling value seems to be right.

And, that ceiling is smaller than the number of people who live in close proximity to each other in cities. The potential facelessness of your neighbors in a city, and its diversity and cosmopolitanism is one reason that it was in cities that written laws displayed in public places emerged as a custom. Societies not bound together by social interaction and kinship needed abstractions which could scale. Laws, kings, and religions are just some of the cultural inventions that were essential to maintain order in a city where strangers interacted daily.

But were these cities really incubators for anonymity? I would argue that the premodern city offered far less anonymity, and therefore privacy than the modern city. Premodern cities were dense, due to limitations in transportation. They were defined by neighborhoods. Additionally, economic activities in cities were often defined by relationships between people, whether it be between a patron and an artisan, or members of a cooperative guild. In some ways, premodern cities were a collection of villages.

What defined the 20th-century was the rise of massive corporations that rationalized economic consumption and production. The supermarket is cheaper than your local green-grocer, but there is also less of a personal relationship between you and the supermarket staff. Similarly, they may not know who you are. Rather than having economic relationships directly to other people, you have an economic relationship with an institution, which acts as an intermediary.

By the second half of the 20th century, individuals in cities could be totally self-sufficient and isolated from other human beings if they so chose when it came to personal relationships. The rationalization of modern life made deep human interaction a choice, and to some extent, privacy was the default state.

The rationalization of economic relations continues. But over the last 20 years, and especially the last ten or so, the default state of privacy has disappeared. If you know someone’s name you can usually find their age, where they have lived their adult life, who they lived with, and who their relatives are. Websites like Zillow can tell you their home-value or when/if they bought their home and for how much. Facebook, Twitter, and other social media make it so you can find out many things about a person.

Recently a friend of mine who became newly single after ten years in a relationship decided to try out online dating (for the first time). One thing he found is that you have to assume that your matches may have Googled you beforehand (presumably this depends on whether the site gives you full name or not). If you are too shy to talk to your neighbors, just look up who lives at the various addresses around you.  Once you have their names you can find out everything else.

Obviously, modern information technology doesn’t make it so that we live in a premodern village. But, it does mean that the faceless anonymity enabled by rationalized modern economics and socio-political systems is stripped away. In its place, you become a set of values for various parameters (age, income, political orientation, geographical mobility). You don’t know people in a tacit and natural manner, you know them through their data.

Whereas the political and social views of most employees of a corporation were out of view in the 20th-century, today many companies are snooping around in Facebook feeds and doing simple background checks. You may not have a personal relationship with a large company, but it has a relationship with the data that it defines you by.

The 20th-century was the century of privacy because the machinery of information distribution appropriate to hunter-gatherers and villages did not scale to cities. And 20th-century technology never caught up to the scale of the cities and economies of that period in terms of distributing information. As the 21st-century proceeds, it seems that information technology is finally now in place.

Open Thread, 5/20/2018

Filed under: Open Thread — Razib Khan @ 3:40 pm

Warren Treadgold’s The University We Need: Reforming American Higher Education is going to come out in early July, but I’ve written my review. Don’t know when NRO will post it. In general, I’m positive. Though Treadgold has some ideological issues with Leftism in the academy, much of the book is apolitical and shines the light structural problems with contemporary academia.

It’s not a secret that I’m a fan of the author’s earlier work, A History of the Byzantine State and Society. So I checked some of the footnotes in The University We Need, and it turns out he’s a skeptic about the accolades given to Chris Wickham’s Framing the Early Middle Ages. Myself, I think both of these huge books are worth reading.

Bernard Lewis has died. He gets a lot of bad press from people like Edward Said of Orientalism fame, and over the last 20 years has become inextricably connected to neoconservatives who cheered on our nation’s foreign adventures. But a lot of his work is pretty interesting, especially the earlier stuff. I like The Middle East: A Brief History of the Last 2,000 Years.

On The Number Of Siblings And p-th Cousins In A Large Population Sample. I can’t say I follow all the mathematical details but jump to equation 7. But this preprint heavily informs Edge & Coop’s How lucky was the genetic investigation in the Golden State Killer case?

The Coming Wave of Murders Solved by Genealogy. The horse has left the barn and the great rush is on. Ultimatley this all going to be a normal part of forensic work soon enough.

I’m not sure that there’s a single fact yet in The Rise and Fall of American Growth: The U.S. Standard of Living since the Civil War that’s surprised me. Is this because so much of this stuff has now percolated across our culture (e.g., the increased demand for horses in the late 19th century due to complementarity with railroads).

That being said there is a lot of specific detail that’s of interest. For example, the proportion of households with telephones during the Great Depression dropped, but those with radios kept increasing as a fraction of the American populace. The reason is that telephones were rented and required recurrent payments, which many families could no longer afford, while radios were purchased once, after which usage was free.

I don’t know much about Jordan Peterson. Curiously the people who talk to me about him the most are moderate liberals who are annoyed about the demonization of him by the further Left. I don’t have much to say, except it’s shocking how many patrons he has, and, the Left-media attacks on him probably are making him more popular.

Men are far more dangerous than women:

Problematic anti-Semitism bill passes in South Carolina:

The Act, which if not challenged in court and struck down as unconstitutional, will require South Carolina’s public institutions of higher education to “take into consideration the [State Department’s] definition of anti-Semitism for purposes of determining whether the alleged practice was motivated by anti-Semitic intent” when “investigating, or deciding whether there has been a violation of a college or university policy prohibiting discriminatory practices on the basis of religion.”

Heavy-handed suppression of anti-Semitism on campus is going to lead to more, not less, anti-Semitism. You know why.

Genetic analysis of Sephardic ancestry in the Iberian Peninsula.

Hybridization and postzygotic isolation promote reinforcement of male mating preferences in a diverse group of fishes with traditional sex roles.

A New Way for DTC? Nathan Pearson, Root Deep Insight.

Was Kevin Cooper
Framed for Murder?

Farmers, tourists, and cattle threaten to wipe out some of the world’s last hunter-gatherers.

May 19, 2018

The material consequences of Rome’s decline

Filed under: Roman History — Razib Khan @ 9:40 pm

The plot at the top is from a Peter Turchin post, History Is Now a Quantitative Science. Peter has been on this for more than ten years now. I’ve long been broadly sympathetic, but of late it’s been nice to see his formal and data-intensive approach take hold and make some waves. Using raw data from a PNAS paper on the concentration of lead in Greenland ice caps one can illustrate the theory of secular cycles, as the western edge of the oikoumene went through periods of rise and fall. I don’t say specifically Rome because as Peter observes the first rise probably had more to do with Carthage than Rome, and the last recovery was particular mild probably because its focus was on the eastern Mediterranean, rather than the west.

As readers of this weblog know this lead data is not entirely new. I remember stumbling on it in The Fall of Rome: And the End of Civilization. It’s just more fine-grained and detailed than what came before. This sort of result definitively convinced me in a flash that the “fall of Rome” was neither fiction nor propaganda, but a true material event.

And yet the materiality is important. Like Song China, the Augustan and Antonine periods were characterized by a phase of intensive coordinated economic activity and productive output that one can’t deny. It’s right there in the material record. But from the perspective of a Christian or a Muslim, the collapse of the power of the Roman state coincided with the rise to power of the most important development in human history: the cultural dominance of singular religious visions.

The point being that when we say that “Rome fell,” it hides within it assumptions of value and importance. History is not fiction and can be understood in all its reality, but it is always critical to expose your assumptions and gain an understanding of the common ground shared between individuals whose viewpoints may differ.


May 16, 2018

Migration at the roof of West Asia

Filed under: Historical Population Genetics,History,Indo-Europeans — Razib Khan @ 10:16 pm
Click to see the full figure

The figure to the left is from The genetic prehistory of the Greater Caucasus. If you are a regular reader of this weblog, or Eurogenes, you can figure out what’s going on, and keep track of the terminology. But in 2018 I think we’re getting to the end of the line in making sense of “admixture graphs” in relation to West Eurasian population structure. The models are just getting too complicated to keep everything straight, and the distinct-populations-subject-to-pulse-admixture seems to be an assumption that may not necessarily hold.

To get a sense of what I’m talking about, the above preprint focuses on populations in and around the Caucasus region. One of the major reasons that this is important is that the Caucasus was and is to some extent a continental hinge, connecting Eastern Europe and the Pontic steppe, to the Near East. The Arab Muslims pushed north of the Caucasus, and came into conflict with the Khazars, while Cimmerians and Scythians moved south from the Pontic steppe.

The elephant in the room is the relevance to the “Indo-European controversy.” Colin Renfrew long ago posited that the Indo-European languages derive from West Asian farmers who expanded into Europe as early as ~9,000 years ago. A rival theory is that Indo-Europeans spread out of the Pontic steppe ~4,000 years ago. In 2015 two major papers suggested that the steppe was a major source of Indo-European expansion. Case closed? This preprint suggests perhaps not.

But we’ll get to that later. What do the results here show? The prose is a little hard to tease apart, but the major issues seem to be that in antiquity, or at least the period they’re focusing on, much of the gene flow seems to have been south (Near East) to the north (through the Caucasus, and out to the north slope). To some extent, we already knew this: the Yamna people of the Pontic steppe have “southern” ancestry from the Near East that earlier East European/Pontic people do not. In this preprint, the authors show that groups such as the Maykop of the north slope of the Caucasus carry Y haplogroups such as G2, and not the R1 lineages commonly found in the steppe. David W. suggests that this confirms that Near Eastern gene flow into the steppe was female-mediated.  This is plausible, but I would caution that Y chromosomes alone can be deceptive, due to the power of particular patrilineages. We’ll probably rely on the X chromosome to make a final judgment.

The plot below shows many of the relationships as a function of location and time. The green component is modal among “Iranian farmers,” the orange among “Anatolian farmers,” and the blue among “Western hunter-gatherers.”

A major aspect of this preprint is that it has to work hard to differentiate two Anatolian farmer-like signals: the first, from Anatolian farmers proper, and the second from the descendants of European farmers, who themselves are a mix of Anatolian farmers with a minority ancestry among the hunter-gatherers. The answers would probably be totally unintelligible if not for archaeology. It’s clear that the steppe people had contact with both European and Near Eastern farmers and that later East European groups that succeeded the Yamna were subject to reflux from Central Europe, and received European farmer ancestry.

Another curious nugget in their results is that there was early detection of both Ancestral North Eurasian (ANE) ancestry and, some East Eurasian gene flow (related to Han Chinese). One of their individuals carries the East Eurasian variant of EDAR, which today is only found in Finns, though it was found in reasonable frequencies among the Motala hunter-gatherers of Scandinavia. Additionally, Fu et al. 2016 found that the ancestors of Mesolithic hunter-gatherers received some gene flow from Eastern Eurasians as well (also in the supplements of Lazaridis et al. 2016).

The authors admit that there is probably population structure among ANE and undiscovered groups of East Eurasians who were traversing the Inner Asian landscape. I think this is all suggestive of some long-distance contacts, though the intensity and magnitude increased a lot with high-density societies and the mobility of pastoralism.

Much of the genetic mixing in the Near East, and to some extent in the trans-Caucasian region, seems to date to the 4th millennium. This is technically prehistory, but it is also the Uruk period. This was a phase of Mesopotamian culture expansion between 4000 and 3100 BC which resulted in replicas of Uruk style settlements as far away as Syria and southeastern Anatolia. There is even evidence of Uruk-related migration to the North Caucasus.

The Uruk experienced abrupt and sudden collapse. Uruk settlements outside of the core zone of Mesopatamia disappear.

It’s the final paragraph that warrants discussion:

The insight that the Caucasus mountains served not only as a corridor for the spread of CHG/Neolithic Iranian ancestry but also for later gene-flow from the south also has a bearing on the postulated homelands of Proto-Indo-European (PIE) languages and documented gene-flows that could have carried a consecutive spread of both across West Eurasia…Perceiving the Caucasus as an occasional bridge rather than a strict border during the Eneolithic and Bronze Age opens up the possibility of a homeland of PIE south of the Caucasus, which itself provides a parsimonious explanation for an early branching off of Anatolian languages. Geographically this would also work for Armenian and Greek, for which genetic data also supports an eastern influence from Anatolia or the southern Caucasus. A potential offshoot of the Indo-Iranian branch to the east is possible, but the latest ancient DNA results from South Asia also lend weight to an LMBA spread via the steppe belt…The spread of some or all of the proto-Indo-European branches would have been possible via the North Caucasus and Pontic region and from there, along with pastoralist expansions, to the heart of Europe. This scenario finds support from the well attested and now widely documented ‘steppe ancestry’ in European populations, the postulate of increasingly patrilinear societies in the wake of these expansions (exemplified by R1a/R1b), as attested in the latest study on the Bell Beaker phenomenon….

But instead of tackling this let’s focus on the paper that came out of the Willerslev group, The first horse herders and the impact of early Bronze Age steppe expansions into Asia. This is a final manuscript in Science. That means it was probably written before The Genomic Formation of South and Central Asia. When it comes to South Asia, the results from the two publications are consanant. There is no conflict.*

More interesting are the results in West Asia, and the linguistic supplement. In the authors note that tablets now indicate an Indo-Aryan presence in Syria ~1750 BC. Second, Assyrian merchants record Indo-European Hittite, or Nesili (the people of Nesa), as early as ~2500 BC.

As suggested in earlier work Hittite remains don’t suggest steppe influence. David W. says:

The apparent lack of steppe ancestry in five Hittite-era, perhaps Indo-European-speaking, Anatolians was interpreted in Damagaard et al. 2018 as a major discovery with profound implications for the origin of the Anatolian branch of Indo-European languages.

But I disagree with this assessment, simply because none of these Hittite-era individuals are from royal Hittite, or Nes, burials. Hence, there’s a very good chance that they were Hattians, who were not of Indo-European origin, even if they spoke the Indo-European Hittite language because it was imposed on them.

The main aspect I’d bring up with this is that in other areas steppe ancestry has spread deeply and widely into the population, including non-Indo-European ones. It is certainly possible that the sample is not needed enough to pick up the genuinely Hittite elite, but I probably lean to the likelihood that the steppe signal won’t be found. It seems that the Anatolian languages were already diversified by ~2000 BC, and perhaps earlier. Linguists have long suggested that they are the outgroup to other Indo-European languages, though this could just be a function of their isolation among highly settled and socially complex populations.

Two alternative models present themselves for these results. The Anatolian Indo-European languages expanded through elite diffusion,  part of the same general migrations that emerged out of the Yamna culture ~3000 BC. The lack of a steppe signal may be due to sampling bias, as David W. suggested, or, more likely in my opinion, simple dilution of the signal. Second, the steppe migrations were one part of a broader palette of population movements and cultural diffusions, and the Anatolian Indo-Europeans are basal to the efflorescence of the steppe derived branches.

The evidence of the explosion of Indo-Aryans in the years after 2000 BC in West and South Asia, as well as the expansion of Iranians across vast swaths of Inner Asia during the same period, suggest to me that Indo-Iranians are most definitely part of the steppe pulse. The connection to the Sintashta charioteers presents itself, and, connections to the Uralic languages indicates incubation in the trans-Volga region.

In West Asia, the Indo-Aryans crashed themselves against the most advanced civilizations of their time. Like the Bulgars, and unlike the Hittites, Indo-Aryan Mitanni was totally absorbed by their non-Indo-European Hurrian substrate. Indo-Aryan linguistic influence was preserved in their names, their gods, and in particular words relating to chariots. And yet in 2017’s Continuity and Admixture in the Last Five Millennia of Levantine History from Ancient Canaanite and Present-Day Lebanese Genome Sequences, the authors observe:

We next tested a model of the present-day Lebanese as a mixture of Sidon_BA and any other ancient Eurasian population using qpAdm. We found that the Lebanese can be best modeled as Sidon_BA 93% ± 1.6% and a Steppe Bronze Age population 7% ± 1.6% (Figure 3C; Table S6). To estimate the time when the Steppe ancestry penetrated the Levant, we used, as above, LD-based inference and set the Lebanese as admixed test population with Natufians, Levant_N, Sidon_BA, Steppe_EMBA, and Steppe_MLBA as reference populations. We found support (p = 0.00017) for a mixture between Sidon_BA and Steppe_EMBA which has occurred around 2,950 ± 790 ya (Figure S13B).

This needs to be more explored. The admixture could have come from many sources. I am curious about the frequency of R1a1a-z93 among modern-day Syrians and Lebanese.

For me these arguments can only be resolved with a deeper understanding of linguistic evolution. The close relationship of Indo-Aryan and Iranian languages is obvious to any speaker of either of these languages (I can speak some Bengali). A divergence in the range of 4 to 5 thousand years before the present seems most likely to me. But the relationship of the other Indo-European languages is much less clear.

One of the arguments in Peter Bellwood’s First Farmers is that the Indo-European languages exhibit a “rake-like” topology with the exception of Indo-Iranian, which forms a clear clade. To him and others in his camp, this argues for deep divergences very early in time.

It is hard to deny that the steppe migrations between 4 and 5 thousand years ago had something to do with the distribution of modern Indo-European languages. But, it is harder to falsify the model that there were earlier Indo-European migrations, perhaps out of the Near East, that preceded these. Only a deeper understanding of linguistic evolution, and multidisciplinary analysis of regional substrates will generate the clarity we need.

* I’m going to skip the Botai angle in this post.

May 13, 2018

Open Thread, 05/13/2018

Filed under: Open Thread — Razib Khan @ 9:23 pm

The University We Need: Reforming American Higher Education is a funny book. The author, Warren Treadgold, is someone I know from his magisterial A History of the Byzantine State and Society. One of the complaints about A History of the Byzantine State and Society is that it’s too dry and academic. The University We Need is not dry at all, unless you are referring to the mordant wit on display.

Since I’ll be reviewing The University We Need for NRO I won’t say much more than that, except that Treadgold is most definitely in a “gives no fucks” mood. Yes, he attacks administrators as you’d expect, but he also slams Hillsdale, the professoriate, and students. He also has opinions about cafeteria food!

Italy’s 5 Star, League Reach Deal to Govern Nation. This sort of Left-Right hybrid to me illustrates that we’re in a “crisis of capitalism,” or more precisely a crisis of Western civilization. Italian total fertility rate is ~1.40. The rest is commentary.

Localizing and classifying adaptive targets with trend filtered regression. In Who We Are David Reich talks about his ambition to create a sort of encyclopedia of human genomic history. But once that history is established, we’ll need to move on to understanding selection. This preprint looks like it will be important.

23andMe Hits Ancestry.com With Patent Suit Over DNA Kit. One thing they are doing is suing over notifying about identity-by-descent. The “non-obvious” reason for awarding the patent is apparently the notification.

Intellectual property is a joke. But it’s also big business.

This week on the podcast we talked about the grandmother hypothesis with Kristen Hawkes. I should have been more aggressive in jumping in to get her to clarify what “life history theory” was. Live and learn.

We are now at 20 podcasts. If you can, please subscribe with iTunes or Stitcher. Also rate us highly and leave positive views if you can!

Carl Zimmer’s podcast has been recorded already, but won’t be dropped until close to when She Has Her Mother’s Laugh is published. We’re also recording a podcast with Patrick Wyman of Tides of History. This should be “evergreen”, at least on the scale of a year, so expect that in June or later.

The next few weeks we’re going to go it alone with just Spencer and myself, talking about a few topics we’re both interested in. It’s a good change of pace. We’ve got some ideas for what we’re going to talk about in June. I think it is most definitely important to follow-up on the Indo-Aryan podcast, which we actually recorded in July of 2017, though we didn’t drop it until 2018.

There was an interesting fiasco on Twitter recently where some semi-prominent people asserted that Andrew Sullivan was against gay marriage. This is really bizarre because Sullivan was a major proponent of the idea before it was ever mainstream, and for a period also got resistance from the more radical anti-bourgeois faction of the gay rights movement.

Anyway, the mistaken tweets occurred because Sullivan is transforming into a hate-figure on the Far Left, and a lot of people are Twitter are stupid and ignorant, so they just inferred facts from their theory that Sullivan is right-wing. Some of these people retracted the falsehood grudgingly but as usual you can see that retweets and likes are/were more evident on the original tweet.

The point is repeating all this is this is how “knowledge” is created now. If you have a prominent Twitter account it’s trivial to inject falsehoods into the debate. I’ve seen people doing this pretty consciously several time (this is really common in anonymous/pseudo accounts).

At the Brown Pundits weblog, I put up a post on this strange Slate piece on how the 1990s TV show Friends is contributing to sexism and homophobia in India. Though ostensibly about India, and narrated by an immigrant from India, the piece is about preoccupation within American culture in 2018.

A publication like Slate is going to get a lot of clicks if they post something about misogyny and homophobia in Friends, but how to make it novel? Pretend it’s actually about India! To me, this is to journalism to science fantasy is to science fiction.

Societies and cultures in relative decline and undergoing stagnation tend to undergo a period of involution. Narcissism writ-large.

I also wrote a post on Brown Pundits on why India did not become mostly Muslim. Need to think a lot more on this. Not all the comments were dumb.

Reading the coalescent chapter in Molecular Population Genetics, and it’s amusing to note that the coalscent’s big advantage over forward-simulations in terms of computational horsepower needed isn’t really that big of a deal today. Even a few years back this was a huge issue. This is like in phylogenetics where everyone runs Bayesian stuff, where 15 years ago people were having a hard time imaging max-likelihood!

While reading Molecular Population Genetics I keep hearing the author’s voice in my head. I think this has to do with the fact that I know the author before I read his books. This didn’t happen when I read She Has Her Mother’s Laugh because I had read Carl Zimmer before I got to know Carl in person. At least that’s my theory (The 10,000 Year Explosion was all in Greg Cochran’s voice).

Reading too much about Rome. So Carthage Must Be Destroyed is in the stack.

A systematic assessment of ‘Axial Age’ proposals using global comparative historical evidence. The argument here is that the “Axial Age” wasn’t a singular time period, but a continous event that spanned thousands of years. I think this is probably right, though “ages” are conceptually useful mental bookkeeping. This is similar to the idea that age cohorts are a real thing, but generations are not.

The Infectious Enthusiasm of Breaking the Bee.

Detection of shared balancing selection in the absence of trans-species polymorphism.

Self domestication and the evolution of language.

I need to set aside a day to catch up on the South Asian Genotype Project (SAGP). Also, figure out which plugin is causing the 500 errors.

May 12, 2018

When writing about India is actually just writing about America

Filed under: Culture,Friends — Razib Khan @ 8:57 pm

The web magazine Slate posted a piece, Friends From India which I had initially thought was a parody. Its subtitle is: “I grew up watching the show in Mumbai. I worry about the damage its gender stereotypes still do there.”

It’s really bizarre. The author is Indian, and supposedly is making a comment about India. But the piece isn’t about India at all, but the worries and concerns of a liberal person in the West. Friends isn’t that important in driving social views in India, and gender relations and attitudes toward homosexuality in India have little to do with Friends. But, today Friends seems retrograde to many American liberals, because of its attitude toward gender relations and gayness, which were mainstream in the 1990s.

So it seems here that to get another piece on Friends and social justice into Slate, they just commissioned a piece that was officially about India, but quite obviously wasn’t.

This gets to a major dynamic in American society today which worries me somewhat: foreign affairs being filtered through purely American concerns and perceptions. Americans care so little about the rest of the world that they turn the rest of the world into the United States in substance, if not exterior styles.

The problem is that we are living through a great transition in the world. America is no longer as much the center, and economic, social, and political, power will rebalance toward Asia. In such a multipolar world pandering to purely American preoccupations will lead to gross misunderstandings and likely catastrophe.

The Roman, the Hun and the sun

Filed under: Roman History — Razib Khan @ 8:23 pm

I chose a fortuitous time to read Kyle Harper’s The Fate of Rome: Climate, Disease, and the End of an Empire. This is a great book, and a nice compliment to Bryan Ward-Perkins The Fall of Rome: And the End of Civilization. Where Ward-Perkins attempts to convince you that Rome did indeed fall, and that that fall mattered, Harper takes it as a given that you accept this position. Rather, he tries to show you in The Fate of Rome that a series of contingent and necessary causal factors set the Roman system up for its fall. The fall of Rome is not just an idea, but a material event that was given a strong push by material factors.

As the The Fate of Rome was published in the fall of 2017, so it was written well before recent work which highlights both the nature and role of steppe barbarians in triggering the changes which we dramatically term the “fall of Rome” and the “barbarian migrations.” A few months ago I wrote about a paper which reported that post-Hunnic people of the Balkans were genetically different from typical Europeans in that they exhibited some East Asian admixture. Harper does assume that the Huns were barbarians whose ultimate provenance was somewhere in the region of modern Mongolia, but emphasizes that their peregrinations transformed them.

As so it did. A new paper in Nature, 137 ancient human genomes from across the Eurasian steppes, nails the overall dynamics. As illustrated in the figure above the early steppe was dominated by peoples of a West Eurasian provenance, while the latter steppe shifted toward a more East Asian shifted population.

These early groups go by various names. But the Cimmerians, Scythians, and Sarmatians have origins on the Pontic steppe. Flourishing in the first millennium before Christ, I should precisely label them “Iranian,” but that might mislead readers a bit since some of these groups were never resident within Iran. The Scythians were a presence across a huge zone of Inner Asia and were a force in Eastern Europe, West Asia, South Asia, and in Eastern Asia. Likely emerging out of the Andronovo culture, genetically the results from the paper confirm early work that Scythians mixed with the local substrate where they went. In this way, they prefigure later steppe populations. Being a nomad was a lifestyle, the genetic correlates to some extent an accident.

In The Fate of Rome  the Huns have a role to play as a push for the migration of Goths into the Roman Empire, which eventually leads to their rebellion and a collapse in both the prestige and military manpower of the Roman state. The genetic evidence above and elsewhere is strongly indicative of the likelihood that the Huns were originally part of the Xiongnu confederacy. As they moved west they mixed with post-Scythian and other Iranian and Siberian elements, and presumably by the time they arrived on European frontier of Rome they had picked up some Germanic and proto-Slavic ancestry. In 137 ancient human genomes from across the Eurasian steppes the authors also report that the East Asian gene flow was somewhat “male-mediated” in the later steppe. Similarly, earlier work on proto-Iranian peoples in the Altai region is strongly suggestive of male-mediation in West Eurasian gene flow.

The obligate and exclusive Eurasian nomad lifestyle was one dominated by men, though as one can see the importance of Genghis Khan’s wives and daughters women maintained independence as well.

For whatever reason, full-blown nomadism only became a feature of the landscape north of what became China in the last few centuries before Christ. The mobile and militarized nomadic lifestyle that emerged in western Eurasia in the years around 1000 BC seem to have taken five centuries to penetrate the far eastern fringes. Until the crushing of the Dzhungar’s by the Manchus in the 18th century, 2,000 years later, the dynamic between nomad and settled was a defining feature of Chinese statecraft and political culture. And, it was also a major feature of nomad culture, because the wealthy Chinese state was an almost irresistible attraction to steppe elites as a source of plunder and tribute.

But human action is not the only relevant parameter in human history.  The Fate of Rome  is fundamentally a work of history, but it also takes ecology and evolution seriously. In fact, it foregrounds them. Kyle Harper makes the argument that the expansionary phase of the Roman Empire was not necessarily coincidental, or at least it was lucky indeed because there was a climatic optimum, similar to the one which preceded the demographic expansion of medieval Europe. In contrast, in the 6th century, the world went through some of the coldest years in the Holocene because of a combination of fluctuations in solar radiation and volcanic explosions. I assume that the likelihood of the latter is Poisson distributed, so the combination of decreased radiation and several successive volcanic events can be chalked up to randomness. But its consequences were not random at all.

The climatic changes can have demographic and social consequences obviously. Desperate armed pastoralists can overwhelm states, and change the course of history, just as peasants can rebel from taxes and subordination. And, pastoralists can also bring Yerisina pestis, the plague. Climate is an abiotic pressure which is to some extent an exogeneous shock which occurs randomly, and does not react to human feedbac k.* Disease though is a biotic pressure, and though it may relate to abiotic forces, human interaction and agency matter quite a bit.

The Fate of Rome clearly hinges on abiotic factors as initial drivers: a good harvest is good for the state. But the biotic factors, disease, are partly under the control of the state. The Romans did not have germ theory, and were under constant stress due to the high pathogen load, especially of the cities. Harper presents the evidence of high mortality within Roman society well. Because of the endemic ubiquity of disease even elites were impacted by it. But Rome was not just affected by endemic ailments, it was subject to pandemics and plagues. Three loom large in  The Fate of Rome:

  • The Antonine Plague, which ended the expansionary phase of the High Empire in the middle to late 2nd century.
  • The Plague of Cyprian of the middle 3rd century which ushered in a period of state collapse.
  • And finally, the Justinian Plague which marked the end of Late Antiquity and the beginning of the “Dark Ages.”

One of the major insights that Kyle Harper reiterates is that these plagues, these pandemics, are a feature/bug of the Roman imperial system. They are not just the consequence of simply settled agricultural society. As described in books such as Pandora’s Seed, agriculture and settled society transformed the lifestyles of human groups, and many diseases which were rare in hunter-gatherer populations probably became common among farmers. But The Fate of Rome the author argues that pandemics were a novel outcome of complex imperial state-systems with long-distance trade-networks. Small-scale pre-state Neolithic chiefdoms did not have the scale and interconnections to foster plague.

Mass pandemics of smallpox, plague, and influenza are then aspects of civilized life, not, settled agricultural life. This puts the argument of Charles C. Mann in 1493 into greater focus. It wasn’t just more extensive and intensive agriculture in the Old World which left Amerindians vulnerable, it was also that the Old World had thrown up several massive imperial systems which had incubated pandemic producing pathogens (smallpox and influenza epidemics were a major issue in New World societies). These were unleashed at once upon New World societies.

It also suggests to us why adaptation seems to be occurring in the last few thousand years. Bouts of plague which persisted for generations may have driven immunological responses.

Kyle Harper also seems to agree with the general thesis in The Fall of Rome that this period in European civilization was in some ways proto-modern, with economic specialization resulting in a modicum of affluence in ways unimaginable in times before, or after. Trade and some level of mass production allowed British peasants to eat off tableware that was standardized, and not homemade. In contrast after Britain’s post-Roman regression a more local economy had to step in. The most curious fact from The Fall of Rome is that pollution in British ponds did not attain Roman levels until the early modern period, with the rise of industrialization. Again and again  The Fate of Rome emphasizes that social and economic complexity achieved in the Roman Empire was not attained in Europe again to the same scale as the early modern period.

Roman wealth was fundamentally due to the returns on scale and specialization that are the hallmark of Smithian growth. Though the Romans did invent a few things, Roman prosperity was not fundamentally driven by innovation. Rather, the Roman peace was a framework for trade and exchange that took advantage of abiotic clement conditions (the Roman climatic optimum highlighted in The Fate of Rome).

But this political system had biotic costs, as well as being subject to biotic shocks. Though Romans may have been wealthier than their Iron Age predecessors in things, and also wealthier than their early medieval successors, they were also a smaller people. Using isotope data Harper suggests that this is not due to Malthusian immiseration as the imperial population pushed up against food supply. Apparently Romans did not subsist on gruel alone, but ate a fair amount of meat, especially pork. Rather it was the high pathogen load enabled by the advancement of Roman urban life and its scale. Rome was a world of intense morbidity.

Unlike physical/abiotic forces biological/biotic pressures on human existence are adaptive. Moderns know this with the rise of antibiotic resistance, it’s the eternal race. The Romans were not aware of the consequences of their means of prosperity, and were not ready for the exogenous shocks of climate and disease which were to perturb their state system.

But The Fate of Rome is not just a story of exogenous factors, climate and disease. Rather, Harper puts into stark relief the variables which might push an empire over the edge, or eat into its seed corn of human capital. That does not negate the fact that endogenous variables matter. The Roman elite of the early centuries exhibited some level of asabiyyah, social cohesion. The Empire was fundamentally not a strong state in comparison to modern ones. It was a thin skein of cities and fortifications binding together an overwhelmingly rural population of villages. Its achievement of peace and prosperity was bound up in an ideology and identity focused project which bound together an elite (or bound together elites).

The origins of this elite were not always arbitrary. Though the Empire was famously cosmopolitan, The Fate of Rome crystallizes something that anyone who had sat back and thought about could see: certain groups bound the imperial state together as a ruling caste. Harper observes that between the reign of Claudius and Phocas, from 268 to 602, 75% of the Emperors were of Illyrian/Balkan stock. That is, 75% of the Emperors were drawn from 2% of the Roman Empire’s territory. The exception being the Theodosian dynasty, which was of Iberian origin, and jumped into the breach after defeat of Valens at Battle of Adrianople.

This is a fascinating fact in and of itself. Harper points out that these Emperors from the Danube frontier did not enrich their own region to the detriment of others. They were ideological heirs of the earlier Roman project, and their identity was as Romans first, Illyrians and Thracians of Latin stock second (or third, after Christianization). But they brought particular skills of administration and an overall martial attitude which served to lead the Empire through a period of greater stress than it had been subject to during the earlier climatic optimum.

The Fate of Rome does not plumb the depths of ideological and social change, but emphasizes their interaction with biotic and abiotic factors. Harper observes that public temple building decreases sharply after the Cyprian plague. Why? Perhaps there was a loss of faith in the old religious institutions. Though popular paganism remained dominant, new elite religious ideologies such as the cult of the invincible Sun and later Christianity came out of the shadows during this period.

These cultural and political aspects remain bit players and mostly offstage in The Fate of Rome. If you are interested in political narrative, than something like Peter Heather’s The Fall of the Roman Empire may be more to your taste. If culture, then Mary Beard’s SPQRBut ultimately social, political, economic, biological, and climatological factors are critical and interconnected. The rise of plague is hard to understand outside of the context of trade, which was enabled by political power and unity. Ecological factors may have driven Yerisina pestis out of its Central Eurasian reservoir, and those ecological factors may have been triggered by climatic variables.

The fall of Rome is a huge topic. I’m just glad that we’re beyond the revision of the previous generation which denied that it happened in the first place. The reason that it occurred is probably contingent in the details, though inevitable over the long-term. All things must end, even the Roman peace.

* This is not totally true, but over the time scales we’re talking about probably mostly true.

May 10, 2018

India as the hydra against Islam

Filed under: History,Islam,Islamicization — Razib Khan @ 9:19 pm

In some versions of the legend of the Hydra, every time you cut off one of the heads of the monster two more grow in its place.

I have been thinking about why and how India remained predominantly non-Muslim despite most of the subcontinent being under Muslim ruling for 500 years (dating from 1250 to 1750 approximately). The contrast here would be most stark with Iran and Turan. While the zone of the Islamic Empire between Mesopotamia and the Maghreb was dominated by a Christian populace which spoke an Afro-Asiatic language, Iran and Turan retained their language and their cultural distinctiveness, as evidenced in the nationalism clear in the Shahnameh.

There was a comment on this weblog that implied India was unique because of violent resistance to Islamicization. This is patently false. To give a concrete example, the region of Tabaristan in northern Iran was dominated by warlords and dynasties which adhered to the Zoroastrian region until the 9th century, 200 years after the Arab defeat of the Sassanians. Despite the inroads of Islam in the 9th century, after more thorough integration into the Abbassid Caliphate, Tabaristan was still throwing up Zoroastrian anti-Muslim warlords into the 10th century.

But most attempts to infer the religious demographics of Iran, which are to a great extent guesswork, suggest that it was in the 10th century the region became majority Muslim. One indication of this that this is so is that this period correlates with a more muscular and resurgent Iranian high culture and reemergence of political non-Arab political power. As Zoroastrianism was no longer seen as a threat to Islam, Persian cultural identity could reassert itself without a non-Islamic connotation (there is in the 10th century a shift away from ostentatiously Arab names by Persian Muslim elites).

Basically, it seems that it took about 300 years for Iran to become majority Muslim. I’ve seen similar numbers for Egypt and the Maghreb, though in the latter region indigenous Christianity became extinct by the medieval period.

There are two related issues that I want to suggest for South Asia: scale and complexity. Though the Indian subcontinent is geographically smaller than the Arab Caliphates as their height on paper, the reality is much of the Near  East and North Africa are empty of people. Islamic rule really consisted of a string of cities and fortifications interlaced over broad swaths of the territory occupied by pastoralists, as well as a few regions of dense cultivation.

Iran, Turkey, and the Arab world consist of between 400 and 500 million people. The Indian subcontinent has 1.7 billion people. The population in the past may have been different, but I think it gives one a rough sense of the differences in magnitude over the long-term.

Second, the social complexity of South Asia is astounding. I say this as a geneticist: the differences between different castes in the same region are hard to believe. Though there is a great deal of ethno-religious diversity in the Middle East, they are not surprising. Arabs engage in a great deal of consanguinity. Ethno-religious minorities such as Copts or Assyrians have less cosmopolitan ancestry than their Muslim neighbors. This is all to be expected.

In contrast, any analysis of ethnic “Telugus” has to take into account local structure because it is so extreme. Dalits are different from middle castes are different from Brahmins. Some of this is due to genetic drift, but much of it is due to continental-scale differences in genetic admixture.

The genetic differences are something us deep about the nature of South Asian social relations. Defection to Islam occurred on the individual scale, but generally, quantity could only be had by mass conversions. Even when groups of people of the same community are of different religions it was probably through mass conversion of particular subsegments.

Which brings me to Bengalis. The Rise of Islam and the Bengal Frontier was written many years ago, and I read it long before I ever knew much about the genetics of South Asians. In it the author explains that the dominance of Islam on the eastern march of Bengal was due to the fact that it was a frontier society that emerged during the period of Islamic rule. Meanwhile, western Bengal was a culture which was in a stationary state.

The ability of Islam to penetrate into the Bengali-speaking peasantry was due to its fluid and unordered character. In contrast in western Bengal, a more traditional South Asia society with well-delineated caste boundaries had already crystallized by the time of the Muslim conquest.

So here’s the thing that genetics adds: the topology of genetic variation of Bangladeshis is totally different than what you see in other South Asians. There’s very little structure. Basically aside from a few half-Brahmins and a small community of Dalits, the 1000 Genomes sample from Bangladesh shows none of the genetic variation partitioned by the community you see in most Indian samples. Or, that you see in the Indian Telugus, Gujuratis and Pakistani Punjabis (the Tamils from Sri Lanka are somewhat less structured, but still have more than the Bangladeshis).

To me, this confirms the thesis of The Rise of Islam and the Bengal Frontier. As a frontier society, eastern Bengal was mixed in a way where the structure socially and genetically that was the norm in most of South Asia by the time the Muslims arrived. Without the powerful collective substructure, Islam was able to swallow up the rural society in toto. Perhaps the best analogy might be to Indian communities in Trinidad, where caste has mostly disappeared, and Christianity has made extensive inroads.

Note: I moderate comments, please don’t stupid spam me.

The bourgeoisie baby blues

Filed under: Economics — Razib Khan @ 8:03 pm

There are those instances when you see a plot that resonates with your experience so much that you don’t need to say anything. You just share it. Those who know, know. Those who don’t know, won’t know until they are in a position to know.

Median household income in the United States today is $59,000. “Household” is a broad category. All families are households, but not all households are families. The median family income is $72,000. If the plot above is correct households in the bottom 25% and somewhere in the top 1% are above demographic replacement. The 1% cut-off is $430,000, and from what I can tell poking around the households making $1,000,000 per year are probably the 0.1%. In other words, between the 75th percentile and 0.10% percentile Americans are below replacement in total fertility.

There is a particular trough between $50,000 and $250,000. From the core of the middle class into the heart of the upper middle class.

From $50,000 a year household income of $250,000 a year may look comfortable, but these are the children of Epictetus. The modern world is filled with those who lack freedom but live with some modicum of comfort, as well as avenues for leisure and self-cultivation. But freedom is reserved for capital, in particular, those with a lot of liquid capital.

It is a truth universally acknowledged that a slave with a substantial income remains but a slave at the end of their days. Their comforts persist only at the sufferance at of those who have inherited or grasped their freedom.


May 8, 2018

The peoples of the Maghreb have some Pleistocene roots

Filed under: Human Population Genetics,North Africa,Population genetics — Razib Khan @ 11:58 pm
Moroccan Berber man

The Maghreb is an important and interesting place. In the history of Western civilization, the tension between Carthage, the ancient port city based out of modern-day Tunisia, and Rome, is one of the more dramatic and tragic rivalries that has resonances down through the ages. Read Adrian Goldsworthy’s chapter on the Battle of Cannae in The Punic Wars for what I’m alluding to (and of course there was Cato the Younger’s dramatic remonstrations).

Later Roman Africa, which really encompassed northern Morocco, coastal Algeria, and Tunisia and Tripolitania, became a major social and economic pillar of the Imperium. Not only did men such as the emperor Septimius Severus and St. Augustine have roots in the region, but these provinces were a major economic bulwark for the Western Empire in its last century. The wealthy Senators of the 4th and 5th century were often absentee landlords of vast estates in North Africa. The fall of these provinces to the Vandals and Alans in the 430s began the transformation of the Western Empire based in Rome into a more regional player, rather than a true hegemon (perhaps an analogy here can be made to the loss of Anatolia by the Byzantines in the 11th century).

Another important aspect of North Africa is that it is the westernmost extension of the region possibly settled by Near Eastern farmers in Africa. The native Afro-Asiatic Berber languages seem to have been dominant in the region despite the influence and prestige of Punic and Latin in the cities when Muslim Arabs conquered the region in the late 7th century. The genetic-demographic characteristics of the region are relevant to attempts to understand the origins of the Afro-Asiatic languages more generally since Berber is part of the clade with the Semitic languages.

A preprint and a paper utilizing ancient DNA have shed a great deal of light on these questions recently. The paper is in Science, Pleistocene North African genomes link Near Eastern and sub-Saharan African human populations. The preprint is Ancient genomes from North Africa evidence prehistoric migrations to the Maghreb from both the Levant and Europe. They are in broad agreement, though they cover somewhat different periods.

The figure below is the big finding of the Science paper:

They retrieved some genotypes from a site in northern Morocco, Taforalt, which dates to ~15,000 years before the present. This is a Pleistocene site, before the rise of agriculture. The Taforalt individuals are about 65% Eurasian in affinity, and 35% Sub-Saharan African. This confirms that the Eurasian back-migration to northern Africa predates the Holocene, just as many archaeologists and geneticists have reported earlier.

The samples from the preprint date to a later time. IAM in the samples dates to 7,200 years before the present, and KEB to ~5,000 years before the present. It seems pretty clear that the IAM samples in the preprint exhibit continuity with the Taforalt samples. Though it is not too emphasized in the preprint the lower K’s seem to strongly suggest that the IAM samples have Sub-Saharan African ancestry, just like the Taforalt samples which are nearly 8,000 years older. In the KEB samples, the fraction drops, probably diluted in part by ancestry related to what we elsewhere term “Early European Farmer” (EEF), related to the Anatolian farming expansion.

Both the Taforalt and IAM samples, in particular, seem to exhibit strong affinities to Natufian/Levantine peoples. Additionally, many of these samples carry Y chromosome haplogroup E1b, just like some of the Natufians. These results indicate that the Natufian-North African populations were exchanging genes or one cline rather deep in the Pleistocene.

Though various methods have suggested that there is a lot of recent Sub-Saharan African admixture, dating to the Arab period, in North Africa, these results suggest that much of it is far older. The Mozabites, as an isolated Berber group, reflect this tendency. Though some individuals have inflated African ancestry due to recent admixture, much of it is older and evener. And yet the Mozabites seem to have less Sub-Saharan African ancestry on average than the IAM sample.

There aren’t enough data points to make a strong inference about the temporal transect, but these few results imply a decline in Sub-Saharan ancestral component after the Pleistocene with further farming migration, and then a rise again with the trans-Saharan slave trade during the Muslim period. Another issue, highlighted in the preprint, is likely heterogeneity within the Maghreb in ancestry (lowland populations in modern North Africa tend to have more Sub-Saharan ancestry due to where slaves were settled).

In the Science paper the authors make an attempt to adduce the origin of the Sub-Saharan contribution to the Taforalt individuals. The result is that there is no modern or ancient proxy that totally fits the bill. These individuals have affinities to many Sub-Saharan African populations.  The Sub-Saharan component is likely heterogeneous, but attempts to model European genetic variation during the Ice Age ran into trouble that divergence from modern populations was quite great. Until we get more ancient DNA there probably won’t be too much more clarity.

On the issue of the Eurasian ancestry, it’s clearly quite like the Natufians. But curiously the authors find that the Neanderthal ancestry in these samples is greater than that found in early Holocene Iran samples. From this, the authors conclude that they may have had a lower fraction of “Basal Eurasian” (BEu) than those populations further to the east. But already 15,000 years ago BEu populations were mixed with more generic West Eurasians to generate the back-migration to Africa. If BEu diverged from other Eurasians >50,000 years ago, then it may have merged back into the “Out-of-Africa” populations around or before the Last Glacial Maximum, ~20,000 years ago.

Finally, the authors looked at some pigmentation genes. Curiously the Taforalt and IAM individuals did not carry the derived variants for pigmentation found in many West and South Eurasians, but the KEB did. This confirms results from Europe, and population genomic inference in modern samples, that selection for derived pigmentation variants is relatively recent in the Holocene.

I do want to add that one possibility about the Sub-Saharan ancestry in the Taforalt, and probably all modern North Africans to a lesser extent, is that it is ancient and local. We now know proto-modern humans were present in the region >300,000 years ago. Northwest Africa may have been part of the multi-regional metapopulation of H. sapiens, as opposed to the Eurasian biogeographic zone that it is often placed, before a post-LGM back migration of Eurasians.

May 7, 2018

Open Thread, 5/07/2018

Filed under: Open Thread — Razib Khan @ 11:29 pm

Longtime readers are well aware that A History of the Byzantine State and Society is one of my favorite books. To understand the Middle East right before the arrival of the Mongols and the emergence of the Crusader states, one has to understand the expansion of Byzantium in the early 11th century, and it’s subsequent regression in the late 11th and 12th centuries. In 2005 I actually did a 10 questions with the author, Warren Treadgold.

So I’m very excited to be reviewing his new book, The University We Need: Reforming American Higher Education, for NRO.

Had a chance to read Matt Hahn’s Molecular Population Genetics. The con is that it’s an $80 book that’s 350 pages. This is not a replacement for Principles of Population Genetics or Introduction to Quantitative Genetics. Rather, as alluded to by the title there’s a lot of focus on molecular evolutionary and population genetics. Imagine a population genetics book written with an assumption that you know what a SNP-chip is and have access to genome-wide sequence data. In some ways, it’s similar to Rasmus Nielsen’s (and Slatkin) An Introduction to Population Genetics. But these books reflect the authors.

For example, if you look up “site frequency spectrum” in An Introduction to Population Genetics there are seven pages. In Molecular Population Genetics there is one page on this topic. Anyone familiar with the work of these researchers would totally expect this. If you are a pop-gen nerd, there’s really no debate. You need to get Molecular Population Genetics or steal it from a friend. But a bigger question is why I recommend seemingly esoteric books to my readers. I say seemingly because understanding the population genetics in the generality makes a lot of the detailed more specifically interesting stuff much more comprehensible.

The readership of this weblog is small but self-selected. If you consider yourself an intellectual person and have some disposable income and leisure you should be developing yourself in various ways outside of the professional sense.  If you are reading this weblog you are likely to be the type of person who wants to understand things not just because one gets paid to understand things, but because understanding things is an end unto itself.

I am privileged to be paid to explore various topics related to certain intellectual interests (human population genomics), but I believe that something would be seriously wrong with me if I limited my inquiries to this narrow topic. Therefore I read a fair amount of history, and take an interest in topics like cognitive science and Biblical scholarship. Part of my attempt on this weblog to is to add population genetics to the list of interests of people who are professionally not engaged with the topic, whether they be in closely related fields (e.g., a theoretical ecologist) or in a totally different line of work (union organizer).

The Neutral Theory in Light of Natural Selection. This review is free. One of the great things about this is that it kind of revived a corner of science Twitter which had started to go into senescence (Patrick Phillips has been at the center of several of these discussions).

Related to our podcast topic from this week, Doc Edge and Graham Coop have read the definitive formal take, How lucky was the genetic investigation in the Golden State Killer case? The TL;DR version is not that lucky. They show formally that with a database of ~1 million individuals with SNP-data it’s likely that you’ll get relative matches that might be useful. More precisely, a database of ~1 million means that there is a ~90% chance of at least one 3rd cousin match. There’s even a 25% chance of a 2nd cousin match! A database of ~5 million gives a 75% chance of a 2nd cousin match, and ~10 million gives a 90% chance of a 2nd cousin match. These are around the range of the databases of 23andMe and Ancestry right now.

As the authors say: “it’s a question of deciding the circumstances under which we as a society want these familial searches to be used.”

Tales of Human Migration, Admixture, and Selection in Africa.

The evolutionary history of human populations in Europe. Preprint by Iosif Lazaridis.

There is a certain number of traditional liberals with a libertarian bent who I’ve always admired. Nadine Strossen is one of those (Wendy Kaminer is another). Strossen is out with a new book, HATE: Why We Should Resist It with Free Speech, Not Censorship (Inalienable Rights). It strikes me this is conservative in the literal sense in that she is attempting to defend a late 20th-century liberalism which is now on the wane.

The Liberal Media Can Have Ideological Diversity Without Conservatives. Two sections jump out at me. First, “the social conservative’s view on fetal personhood is unfalsifiable — and does boast a significant constituency — but it doesn’t generally lend itself to novel or engaging debates.” The issue with abortion is not about debating, as much as it is important to not always put forward writers who implicitly assume that the pro-choice position is the only view that one might entertain. I’m skeptical of some of the leaps that pro-life writers make based on their political position…but then, I’m not pro-life. It’s important to at least know the views of other people.

Second, the author suggests that Left-wing socialists who believe that the people should control the means of production (as opposed to simply redistributive socialism as is the case in Scandinavia) should be given a fair hearing, though they observe “concentrating financial power in the state apparatus has often been an invitation to tyranny.” Yeah. That.

Pretty straightforward establishment liberals, such as Matt Yglesias, are starting to assert that publications like The Atlantic and The New York Times are equivalent to National Review, in their ideological valence (the argument being that they shouldn’t have to hire conservatives since they’re liberal publications). Conservative critics have long asserted this, but now liberals are agreeing.

Conservatives have lost the universities and the press. Both these institutions don’t even make a pretense at evenhandedness at this point. The broadly liberal center is eroding. I suspect that people like Nadine Strossen will be viewed in the future like Cato the Younger.

Stuff You Missed in History Class podcast, Mohenjo Daro. People don’t really know much.

Interviewing Carl Zimmer for the podcast this week. Taking suggestions for questions to ask him (we have a finite time so might not get it in….)


May 2, 2018

The Insight, Episode 19: Roberta Estes, the Golden State Killer, and forensic genetics

Filed under: Podcast,The Insight — Razib Khan @ 11:26 pm

Last week Spencer & I took a break from The Insight. We’re at 71 iTunes ratings. I would appreciate it if readers of this weblog could help us make it to 100 (then I’ll stop pestering you). Also, we only have 5 reviews on Stitcher.

This week we’re talking to Roberta Estes about the arrest of the suspect in the “Golden State Killings”. We kind put this together really quickly since it seemed relevant, and Roberta, Spencer and I have some competency in this area (we’ve all been talking to science journalists). The biggest takeaway from our conversation is that we were a little surprised that it took this long to apply 21st century genomics to forensics.

When I first heard about the arrest I told my wife that it probably was due to a relative match on something like GEDMatch. After the media reported that it was a “new method” I dismissed my supposition because relative matches aren’t a new or novel thing. Well, it turned out that’s exactly what they were talking about!

A lot of the story here is how law enforcement snapped a bunch of pieces together that were out there. The horse has left the barn, and everyone is trying to figure out how to deal with it.

May 1, 2018

Hui have a lot of West Eurasian Y chromosomes

Filed under: China genetics,Hui — Razib Khan @ 1:26 am
O C R1a R1b R2 E1b G H I1 I2 J1 J2 L N Q T Total N
Han 258 12 2 2 2 1 1 2 1 1 7 9 2 300
Hui 24 7 21 1 9 1 3 1 1 4 1 11 1 3 14 4 106
Tibetan 49 11 18 1 1 3 3 3 3 7 1 100

It’s been a while since I checked in on the genetics of the Hui people. I found the paper, Analysis of 17 Y‐STR loci haplotype and Y‐chromosome haplogroup distribution in five Chinese ethnic groups. About 50% of the Y chromosomal haplogroups are normally classified as “West Eurasian” (R, E, G, I and J). But curious a fraction of the Han have these too, as do some Tibetans.

Additionally, know that some Mongols also have R1a1a. It’s hard to differentiate different periods of admixture. But to me the presence of R2 and J2 point to a Central/South Asian origin of a lot of the Hui R1a as well.

April 30, 2018

Is American genetic diversity enough?

Filed under: Historical Population Genetics,Human Genetic Variation — Razib Khan @ 8:51 pm

In the nearly 20 years since the draft of the human genome was complete,* we’ve moved on to bigger and better things. In particular, researchers are looking to diversify their panels of human genetic diversity, because of differences between groups matter. You can’t just substitute them for each other genetically.

There have been efforts to diversify the population panels recently, but that prompts the question whether American population coverage is sufficient. My first thought is that the genetic diversity in the USA is probably getting us 90% of the way there. Consider Spencer’s comment about Queens, it’s the most ethnically diverse large conurbation in the country.

There are some gaps though. In Who We Are David Reich points out the distinctiveness of Indian population genetics. The subcontinent has lots of large census populations which have drifted upward deleterious alleles due to long-term endogamy. And, many of these populations don’t have a strong representation in the Diaspora.

In contrast, much of the rest of the world is panmictic enough that an American panel can pick up most of the variation. American Chinese are skewed toward Guandong and Fujian, but a substantial number of people from other parts of China have arrived in the last generation. Regional structure is not so strong that you’ll miss out on too much, aside from very rare variants which are more extended pedigree scale rather than population scale.

There are small populations such as Hadza, Khoikhoi, and Pygmies in Africa which are probably going to be missed by American population panels, but the total census size of these groups is pretty low (for comparison, there are 1 million Pulayar Dalits in the state of Kerala alone). Much of the rest of Africa is West African variation well represented in African Americans, and Bantu and Nilotic variation probably captured my immigrant communities.

I’d propose supplementing American genetic diversity with sampling Cape Coloureds in South Africa.

* No discussions about how the genome isn’t totally complete. I know that.

Diaspora culture are often more conservative

Filed under: Culture,History — Razib Khan @ 8:45 am

Zach made a comment below about conservatism and Diaspora cultures. There are two trends one has to highlight here. One the one hand Diaspora cultures often exhibit synthesis with host cultures and can be quite novel and innovative.

But there is another trend which is a cultural universal: Diaspora cultures often exhibit archaism and crystallize old-fashioned norms and practices. To give a concrete example foot-binding persisted the longest, down to the 1970s, in the Chinese communities of Borneo. The French of Quebec is peculiar in part because it preserves characteristics of older French dialects. The same is true of some Anglo-American English dialects.

April 29, 2018

Open Thread, 04/29/2018

Filed under: Open Thread — Razib Khan @ 10:05 pm

One of the strange things about getting old is that your friends start to become kind of a big deal. Matthew Hahn has a new book out, Molecular Population Genetics. If there is one single reason I keep blogging, it’s to get awareness of the field of population genetics to spread beyond the small circle who are “in the know.” I joked on Twitter that buying this textbook is like spending money to talk to Matt about pop-gen, and that’s surely worth it.

Another one for the stack!

Speaking of worth it, Kyle Harper’s The Fate of Rome: Climate, Disease, and the End of an Empire is definitely worth a read. Not done, and I’m not sure it’s better than The Fall of Rome: And the End of Civilization. Perhaps my issue is that exogenous shocks are to be expected in my view of the world. Though the details in The Fate of Rome are novel, the general thesis and framework were what I’d assumed were taken for granted.

What Happens When Geneticists Talk Sloppily About Race. I don’t think that David Reich was sloppy…though the op-ed was edited in a way that was confusing. That being said I’ve heard through the grapevine that some prominent human population geneticists may write a response to David’s op-ed, which is something I want to see. Part of me still thinks that these vigorous public discussions are important (another part of me just thinks that when Sulla or Marius take over all this old-fashioned fixation on truth will be irrelevant).

One thing stated in the piece above is that regular people have a Platonic model of race. This is true. But it is also a fact that geneticists have not done a good job of explaining to the educated public what population structure is, and why it’s not trivial or arbitrary. I know this from personal experience over 15 years interacting with people about genetics online (some of the funniest interactions are on Facebook where a person of professional class background/status “genetics-splains” me about how I don’t understand the extent [lack] of human genetic variation and how arbitrary population cluster identity is).

With The Genomic Formation of South and Central Asia I obviously think we have the broad outlines of the peopling of South Asia in hand. There will be lots of detailed elaborations of how/what happened, but I think the big picture is nailed down.

That being said some of the objections remind me a lot of Creationist tendencies. Creationists often focus on weak points and hammer in on them over and over.

One of the weird things about Indian genetics is that a lot of people think new research will overturn Hindu nationalism. But I know several Hindu nationalists, and privately they tell me that most Hindu nationalists don’t care about these abstruse issues, and many of the more intellectual ones don’t have a major problem with the science.

GEDmatch, Ysearch and the Golden State Killer.

Anthropogenic habitat alteration leads to rapid loss of adaptive variation and restoration potential in wild salmon populations.

Bracketing phenotypic limits of mammalian hybridization.

A few people have asked about the podcast. We skipped a week, but we’ll be back. Taking some feedback in relation to various aspects of the show. A common issue seems to be that my voice is too quiet though Spencer’s is “just right.”

Again, if you use Stitcher or iTunes please remember to give us positive reviews and 5-stars!

If you have ideas for shows, we’re game.

April 27, 2018

Why Bronze Age steppe people replaced the farmers they conquered

Filed under: Historical Genetics,History,steppe — Razib Khan @ 9:59 pm

One of the major revisions in my own mind about the demographic and historical processes of the Holocene in relation to humans has been the reality that large and dense agglomerations of agriculturalists could be marginalized by later peoples, to the point of having a smaller genetic footprint in the future than anyone might have imagined. If you had asked me ten years ago I just wouldn’t have believed that the first farmers of Europe or South Asia wouldn’t account for the vast majority of the ancestry of the contemporary populations of the region. By “first farmers” I don’t even mean migrants. At that point, I had assumed a primarily Pleistocene indigenous hypothesis for the origin of Europeans and South Asians, with farming diffusing through a mixture of a few migrants along a demographic wave of advance.

That’s not what it looks like according to ancient DNA. In Northern Europe, it seems that around half or more of the ancestry is due to the incursions of a pastoralist steppe population during the Bronze Age. In Southern Europe and South Asia, the fraction is closer to 10-25%. But even in the latter case, the fraction of steppe ancestry is far higher than I had expected.

I had assumed that the steppe migrants would contribute 1-5% of the ancestry of Europeans and South Asians and that the spread of Indo-European languages was a matter of elite transmission and emulation. Think the Hungarians, for example, as an example of what had assumed.

So what explains what really happened?

During the Mongol conquest of Northern China Genghis Khan reputedly wanted to turn the land that had been the heart of the Middle Kingdom into pasture, first by exterminating the whole population. Part of the motive was to punish the Chinese for resisting his armies, and part of it was to increase his wealth. One of his advisors, Yelu Chucai, a functionary from the Khitai people, dissuaded him from this path through appealing to his selfishness. Chinese peasants taxed on their surplus would enrich Genghis Khan far more than enlarging his herds. Rather than focus on primary production, Genghis Khan could sit atop a more complex economic system and extract rents.

Most of you at this point can see the general framework then. For thousands of years, pastoralist people of the Inner Asian steppe and forest would extract rents out of the oikoumene by threatening them with force. The reason the East Roman Empire did not face the Hunnic onslaught during the lifetime of Attila is that they paid the horde tribute. Imperial China did the same during some periods. In other instances, civilized states found in the barbarians of the steppe useful confederates. The Tang dynasty did not collapse during the 750s because of the intervention of the Uyghurs, who suppressed the rebellion of An Lushan. In 9th century Baghdad the rise of the Turks was enabled by their usefulness in court politics and distance from any given faction.

The rise of the “gunpowder empires” during the 16th century and the eventual closing of the Inner Asian frontier with the crushing of the last embers of the Oirat confederacy between the Russian and Chinese Empires in the 18th century marked the end of thousands of years of interaction between the farmland and pasture.

But this makes us ask: when did this dynamic begin? I don’t think it was primordial. It was invented and developed over time through trial and error. I believe that the initial instinct of pastoralists was to turn farmland into pasture for his herds. This was Genghis Khan’s instinct. The rude barbarian that he was he had not grown up in the extortive system which more civilized barbarians, such as the Khitai, had been habituated to.

In these situations where pastoralists expropriated the land, there wouldn’t have been an opportunity for the farmer to raise a family. Barbarian warlords throughout history have aspired to be rich by plundering from the civilized the peoples…but would the earliest generations have understood the complexity of the institutions that they would have to extract rents out of if there wasn’t a precedent?

Instead of conventional historical dynamics of predatory elites and static peasantry, a better way to understand what occurred with the incursion of steppe pastoralists during the Bronze Age might be a simple ecological model of intra-specific competition. In a pre-state society defined by clan and tribal ties, steppe elites may have seen the farmers who were earlier residents in the territories which they were expanding into as competitors rather than resources from which a life of leisure might be obtained. In other words, instead of conquest, the dynamic was of animal competition.

Of course, pre-modern societies did not have totalitarian states and deadly technology. Rapid organized genocide in a way that we would understand was unlikely to have happened. Rather, in a world on the Malthusian margin, a few generations of deprivation may have resulted in the rapid demographic extinction of whole cultures. You don’t need to kill them if they starve because they were driven off their land.

In fact, we have some precedent of this historically. The Spaniards were intent on extracting rents out of the native peoples of the New World and living a life of leisure, but in many areas disease and exploitation resulted in demographic collapse. Imagine a conquest elite as vicious as the Spaniards, but without thousands of years of precedent that conquered peoples were more useful alive rather than dead. 

Addendum: The fraction of haplogroup M, which is probably derived from Pleistocene South Asians, is greater than 50% in places like Sindh. This indicates that the steppe migrations were strongly male biased in the initial generations.

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