The Neanderthal-modern human handover

We live in a time of transitions when it comes to Neanderthals. Since the 2010 discovery of strong genomic evidence for Neanderthal ancestry in most humans they’ve been…humanized. This was pretty much inevitable, but, I also think it was right. Neanderthals were a big-brained human species which dominated much of Eurasia for hundreds of thousands of years. Their culture did exhibit a certain stasis, but then so did that of our modern African ancestors ~200,000 years ago.

There has been a recent debate about how far back the divergence between Neanderthals and modern humans goes back. My own views is that it’s probably further back than 500,000 years, perhaps closer to 750,000 years, but that there may have been ancient gene flow between lineages as well.

A new paper is now out which suggests that Neanderthals persisted in southern Spain for 3,000 years after they disappeared elsewhere, Precise dating of the Middle-to-Upper Paleolithic transition in Murcia (Spain) supports late Neandertal persistence in Iberia. Obviously, I can’t evaluate the taphonomy and all that. There have long been debates by paleoanthropologists about this region and its Neanderthal habitation (some earlier dates suggested Neanderthals persisted down to 29,000 years ago in southern Spain, but those seem to be rejected). What I can say is that it is entirely expected that the Neanderthal range as it contracted would exhibit an s-shaped trajectory, with a tail where they persisted as relic populations in areas which they were particularly well adapted to.

As paleoanthropology and genetics progress I’m rather sure that we’ll drill-down on very detailed dynamics of interaction, and local succession and replacement. Though humans leave cultural artifacts behind, as a rule the first and last fossils in paleontology usually underestimate the time span that a species flourished. I wouldn’t be surprised if the same applied to Neanderthals, and some day someone with a suspiciously high Neanderthal ancestral fraction was sequenced or genotyped who lived just before the Last Glacial Maximum.

Also, I should mention for those of you looking for a pre-Christmas gift, my company’s Neanderthal product (which does a functional analysis of a set of characteristics where modern humans segregate ancestral and derived variants from the two lineages) can be had for $29.99, as Helix is discounting the $80.00 kit cost (the same applies to the $39.99 Metabolism product, though if you bought Neanderthal earlier then Metabolism is always$39.99 since Helix has banked your data).

People keep asking us the details of the Helix-Insitome relationship and how it works. So we decided to write a blog post addressing that (it’s very short), How does Helix work?.

P.S. we’re probably the only start-up in the world where regular office conversation occurs about Neanderthals.

Against the rectification of names of the enemy

Since the beginning of this weblog, a particular tick that is common to humans emerges over and over. A tick that is seductive, inevitable, and which I periodically react negatively to (and surely do engage in). That tick is the one where peculiar or exotic terms, or common terms in specific senses, are deployed to demarcate ingroup vs. outgroup.

This is clearly illustrated by example. Libertarians will often call non-libertarians statists. In some ways, this is a defensible term descriptively. But statists never call themselves statists, and often are confused what that even means. Really the term “statist” is just a way you can tell other libertarians that this person is not of the tribe. It’s not about communicating with the statist in question. It’s about labeling them…a witch!

Another example is ally. This is a banal and general word, but on the cultural Left it’s become transformed into a very specific thing. If you are a white male, you are by constitution an oppressor with privilege, so you must by necessity aim toward being an ally. Ally here means those with privilege joining the struggle against oppression and the liberation of marginalized people.

Almost all of the above terms are pretty standard English words, but bundled together into that paragraph you know the perspective and Weltanschauung it’s expressing.

In the United States those who oppose the right to an abortion because they think the fetus is a person define themselves as pro-life.  Those who support the right to an abortion define themselves as pro-choice. Pro-choice people sometimes call pro-life people anti-choice, while pro-life people call pro-choice people pro-abortion. The terms themselves are not important as descriptions. Rather, they’re about tribal mobilization.

On occasion, I’ve seen the term TERF, for trans-exclusionary feminist. The people who are called TERFs never call themselves TERFs. Often people who are denounced as TERFs don’t see to be TERFs at all.

When someone brings up the term “civic nationalism,” I’m usually pretty sure that that person is probably a white nationalist, because that’s a term that they seem to use a lot (to describe non-racial nationalists). People who are civic nationalists don’t describe themselves as such in normal conversations.

Because my views are generally more conservative than liberal people on the Right often believe that I am aware of all the tribal divisions and lexical nuances deployed by conservatives today. Or, more honestly people who spend a lot of time reading and discussing politics online with the tribe. I have finite time, I don’t really really track of all the new fashionable terms. Political philosophy and history interest me, but the contemporary ephemera, not so much. One of the most irritating aspects of “Neoreaction” was that they had all those terms which made no sense to outsiders without a glossary.

This sort of behavior makes sense ingroup. But when you start spouting off in public forums with new-fangled vocabulary accessible to the initiates you exclude them. Which is fine, but you also make it clear you just want to hear yourself talk.

Though sometimes scientists are guilty of this sort thing, by and large the utilization of words in a peculiar context has a precise meaning which is clear and distinct. For example, the term heritable. Transformed into heritability, it is the proportion of variance in the phenotype explained by variance in the genotype. Now could say “the proportion of variance in the phenotype explained by variance in the genotype” every time, but it’s usually easier just to say “heritability.”

I’ve made it pretty clear I take a dim view of the prospects for this liberal democracy of ours over the next generation or so. A day shall come when you stand with the Frost Giants or you stand with the Aesir. There’s really no avoiding a choice. I would recommend on that day pick you pick the strongest side, not who you think is the right side. Power is truth, truth is not power.

But this day is not that day. Until then there is still time to listen and cultivate one’s mind. Let’s dispense with bleeding private language into public. It’s just unseemly.

Cystic fibrosis as the sickle-cell anemia of the north

Cystic fibrosis is one of those ‘classical’ recessive diseases you learn about in medical genetics. It’s frequent enough that doctors will always be interested in it, and its inheritance pattern is relatively simple, following a rough Mendelian pattern of recessive expression. The reality is a little more complicated than that though, as there are different mutations in the CFTR gene, and some variants can complement so that two carriers don’t necessarily have a risk of producing a child which expresses the disease.

But CF is also interesting from an evolutionary perspective. Why is such a lethal disease present at such high frequencies in Northern Europeans? On the order of 1 out of 25 Northern Europeans carry a mutant allele on CFTR. Apparently, 1 in 19 Irish carries a mutation for CF, while Finland it’s prevalent at a frequency of around 1 in 90, which is actually in the range of non-European populations.

Though it is well known that inbred populations can manifest high frequencies of deleterious alleles, as a whole Northern Europe is not an inbred population. So what’s going on? One hypothesis is that heterozygotes for CF (carriers) have a higher fitness than wild-type individuals, so the low but persistent frequency of CF expressing individuals is an outcome of this overdominant effect. The analogy then presents to sickle-cell anemia.  Heterozygotes are more resistant to malaria, an endemic and pervasive disease in much of the tropics and subtropics.

So what might be causing the high frequency of mutant CF alleles in Northern Europe? One candidate has been tuberculosis, a very common disease in the recent past in Europe. A new paper out of Brazil supports this contention with epidemiological methods, Cystic fibrosis carriership and tuberculosis: hints toward an evolutionary selective advantage based on data from the Brazilian territory:

Applying spatial epidemiology, we studied the link between CF carriership rate and tuberculosis (TB) incidence in Brazil. We corrected for 5 potential environmental and 2 immunological confounders in this relation: monthly income, sanitary provisions, literacy rates, racial composition and population density along with AIDS incidence rates and diabetes mellitus type 2. Smoking data were incomplete and not available for analysis.

A significant, negative correlation between CF carriership rate and TB incidence, independent of any of the seven confounders was found.

The immediate objection is that one may not have controlled for all the confounds. Though do note there are molecular biological rationales for why CFTR heterozygotes may be more fit when infected with tuberculosis.

All that being said Brazil is a diverse place, and it is hard to imagine there might not be a confound out there geographically. Fortunately, we won’t be doing a randomized controlled field trial by infecting individuals with tuberculosis, so we’re just going to have to keep looking at these correlational studies.

Something has to be driving selection for this nasty disease as part of the genetic correlation.

Open Thread, 11/19/2017

So we put up a 3rd reviewer mug. Kind of an “inside joke”, but we liked it. One thing we have noticed: people really like the DNA helix logo. They click it. They buy it. More visual, less wordy.

One thing that’s funny, when it paternal haplogroups I1 clicks a lot, but they never buy (in contrast to R1b).

Thousands of horsemen may have swept into Bronze Age Europe, transforming the local population. The piece is pretty expansive, though something of a mess. But it’s a mess because there are still unresolved issues.

There’s a Digital Media Crash. But No One Will Say It. Privately my friends in the media tell me exactly this. It’s going to get worse before it gets better. There are many reasons, but it’s happening.

The Evolutionary Genomic Dynamics of Peruvians Before, During, and After the Inca Empire. Similar thing in Mexico: old population structure is still there!

Singleton Variants Dominate the Genetic Architecture of Human Gene Expression. Genomics is a little overhyped, at least in evolution, but it can really do incredible things nailing down the specific details of what’s going on.

The nature of nurture: effects of parental genotypes and Estimating heritability without environmental bias.

Don’t throw out the sympatric species with the crater lake water: fine-scale investigation of introgression provides weak support for functional role of secondary gene flow in one of the clearest examples of sympatric speciation.

I’ve spent a little time reading Oathbringer this week, mostly before I go to sleep. It’s a little hard to keep track of everything because it’s been seven years since the first book and over three since the last one. Since Brandon Sanderson projects ten books in the series I doubt I will finish this out. At the current rate of production I will be thinking about retirement when the Stormlight Archive is near completion!

But reading Oathbringer it did come to my mind that Sanderson has done a really good job in building a world which is fundamentally not just a European Middle Ages retread, as is the norm in much of fantasy. There are so many new words and characters to keep track of I think I didn’t internalize this in the earlier books. So I did a little Googling and found that Sanderson was trying to do the same thing that Frank Herbert did in Dune, by creating a whole new and novel ecology.

Secondly, he has mentioned that most of his characters are not white and that he has struggled to make sure that they are not depicted in stereotypical European fashion in cover art. The primary protagonists are in fact a people who he imagines to be a hybrid between East Asians and Middle Easterners (his time in Korea as a Mormon missionary inflected his world-building), though that is simply the closest analog. He specifically states that the one human race without epicanthic folds, and look the most European in feature and complexion, are often assumed to be East Asian in by readers because of their exoticism and name (Shin).

Charles Manson has died. I haven’t read it, but have heard good things about Jeff Guin’s Manson: The Life and Times of Charles Manson (it seems like it’s a cultural history).

Precise dating of the Middle-to-Upper Paleolithic transition in Murcia (Spain) supports late Neandertal persistence in Iberia. What we’re learning is that our patchy understanding of the human past also understates how patchy and uneven many dynamics were.

The day the Pintupi Nine entered the modern world. The story of nine people who were totally isolated from the modern world until 1984. They were scared when they met relatives who had lived in a town. To convince them to stay the relatives had them taste sugar.

PCA remains the swiss-army-knife to explore population structure

I put up a poll without context yesterday to gauge people about what methods they preferred when it came to population genetic structure.* PCA came out on top by a plural majority. More explicitly model-based methods, such as Structure/Admixture, come in right behind them. Curiously, the oldest method, pairwise Fst comparisons (greater Fst means more variance partitioned between the groups), and Treemix, the newest method, have lower proportions of adherence.

Why is PCA so popular? Unlike Treemix or pairwise Fst you don’t have to label populations ahead of time. You just put the variation in there, and the individuals shake out by themselves. Pairwise Fst and Treemix both require you to stipulate which population individuals belong to a priori. This means you often end up using PCA or some other method to do a pre-analysis stage. Structure/Admixture model-based methods make you select the number of distinct populations you want to explore, and often assume an underlying model of pulse admixture between populations (Treemix does this too when you have an admixture edge).

PCA is also better at smoking out structure than Structure/Admixture for the same number of markers, and, it’s pretty fast as well. This is why the first thing I do when I get population genetic data where I want to explore structure is do a PCA and look for clusters and outliers. After this pre-analysis stage, I can move onto other methods.

Further reading:

* I stipulated “genotyped-based” methods to set aside some of the new-fangled techniques, which often assume phasing and analysis of haplotypes, such as Chromopainter or explicit local ancestry deconvolution (some local ancestry deconvolution does not require phased haplotypes, but the most popular do).

Domestication of Rice in the Amazon

A new paper, Evidence for mid-Holocene rice domestication in the Americas, suggests that the Amazon basin was very culturally productive in the pre-Columbian period. What happened? From the conclusion:

The arrival of Europeans to the American continent in AD 1492, with the consequent population decimation and impact on cultural practices, caused the domesticated traits to gradually disappear. The loss of domesticated varieties is a phenomena that has also occurred for other indigenously domesticated species in both South….

One of the novel arguments in Charles C. Mann’s 1491 is that our idea that the Amazon basin has always been a pristine wilderness could be incorrect. Mann relays the theories of revisionist scholars who argue that at one point in history much of the basin was subject human landscape manipulation, with concentrated burnings allowing for increased productivity in the normally poor soil of the region. Of course, this triggered a counterattack from classical scholars.

If these results about rice domestication are confirmed and become solid I think this would lean toward supporting the arguments of the revisionists, whose side Mann seems to favor in any case.

A major general theme in 1491 is that the Columbian Exchange was a disaster for New World peoples, though relatively positive for the Old World. European access to land surplus in the New World has been given as one reason for the economic takeoff of this region (“ghost acres”), while maize introduced into China was responsible for its great population expansion in the centuries leading up to 1800.

In contrast, the consensus seems to be that New World populations suffered massive population declines (some of this has been confirmed by genetic evidence) driven in large part, though not exclusively, by introduced Old World diseases. Mann argues that early fantastical reports of a dense network of villages along the Amazon (which may have fueled legends of El Dorado) actually reflect the reality that in the 16th century the riverine civilization had not collapsed due to disease. At least not yet.

Let’s stipulate that rice domestication in the Amazon was occurring before 1492. This adds another independent domestication event during the Holocene. Basically, agriculture seems to be something that pops up over and over again after the end of the last Ice Age. Why? As I have suggested before a lot had changed since the previous interglacial over 100,000 years before the present. Our cognitive orientation and our cultural toolkit seem to evoke agriculture relatively quickly and independently.

Second, the indigenous peoples of the Amazon today are predominantly hunters and gatherers or slash & burn agriculturalists. Relatively simple societies. In 1491 the author outlines that that mass death often resulted not directly from disease, but the fact that the debilitation of large proportions of the population then led to famine, which led to social disruption and institutional collapse, which then fed into more death and destruction. Today we perceive the Amazonians as “ancient” and “primal” nomads of the forest, just as their tropical homeland is seen to be eternal and everlasting. This, despite the fact that many of them even today are agriculturalists, albeit of a low-intensity sort. But as they are, perhaps so we could be. Complex societies seem to unravel awful quickly when subject to exogenous “shocks.” Perhaps we should be grateful for our “Pleistocene minds.” You never know when a swiss-army-knife mind is going to come in handy….

Note: the natives of the Amazon are unique in the Americans is having a very basal Asian ancestry in their heritage.

(via Dispatches from Turtle Island)

The world of Tolkien coming to the smallscreen

Unless you are hiding under a rock right now you may have heard that Amazon seems to have purchased the rights for the world of The Lord of the Rings. My understanding is that this deal does not cover The Silmarillion (unfortunate, but perhaps for the best as I’m not sure I’d want to see a dramatization of The Children of Hurin). So perhaps one can imagine a series about Aragorn’s earlier adventures in Gondor? If I had my pick though I’d set something during the time of Gil-galad. The Second Age hasn’t be explored in narrative, so it’s a relatively blank canvas, and like The Lord of the Rings it ends in an existential climax.

Why is this happening? Read the story I linked to above. But clearly it’s because of Game of Thrones. As some of you might know George R. R. Martin attempted to develop his works for film in the wake of Peter Jackson’s success. But A Song of Ice and Fire was too sprawling, or more concretely it’s budget would have been outlandish if one wanted to depict it accurately.

In one volume the three book in The Lord of the Rings comes in at a little over 1,000 pages. In contrast the completed books of A Song of Ice and Fire are already more than 4,000 pages.

But this is in some ways the weakness of an attempt to turn The Lord of the Rings into something equivalent to Game of Thrones: the characters are not nearly as well fleshed out in their humanity as those of A Song of Ice and Fire. Tolkien and Martin share similarities in world-building, with a punctilious attention to detail, and a de-emphasis on magic as a deus ex machina.

But when it comes to good and evil Martin’s distribution is more uniform while Tolkien’s is bimodal. The shades of grey found in A Song of Ice and Fire are great raw material for character arcs in episodic television which sprawls over a decade. In contrast, The Lord of the Rings was compressed into three films, so the relatively simple and stark characterizations were good fits in the context of the world-building and plot. I don’t envy the actor who has to play Viggo Mortensen’s role, nor do I want to imagine the abuse writers or show-runners who want to add moral complexity and ambiguity to Aragorn’s character are going to experience from the hardcore fans.

In other news, you can now get a copy of Brandon Sanderson’s Oathbringer. One of the greatest fantasists of our time, albeit he produces works which are Heavenly Father approved! (I don’t state this as a criticism, it’s just that the God of Sanderson’s universe couldn’t even conceive of a creature like Cersei Lannister, let alone create her)

Addendum: The Hobbit films that Peter Jackson produced in this decade are correctly described as bloated affairs. The book didn’t have enough source material to create a plot that extend across three films. But, also note that there isn’t much character development or difference in many of the characters who spanned both groups of films. Part of is that Gandolf is an immortal demigod, while elves such as Elrond and Galadriel are thousands of years old (Galadriel is one of the oldest beings in Middle Earth, she was born ~7,500 years before the events Jackson’s films). It’s hard to imagine a lot of character development over a few decades for such individuals, but one could imagine implications of having lived thousands of years and how it might drive you somewhat crazy (R. Scott Bakker explores this in detail in The Great Ordeal).

My son in the genetics history books

Just saw today that my son’s prenatal sequencing was mentioned in DNA: The Story of the Genetic Revolution:

The ethics of sequencing a presumably health fetus will be debated for years to come. But the day of doing is already here. Razib Khan, a thirty-something graduate student and blogger, decided to sequence his first child’s genome while his wife was still pregnant. Although one instance of whole-genome sequencing in utero was reported in the New England Journal of Medicine in 2012, that had been done to supplement a positive cytogenetic result….

I want to correct the record for future printings: my first son was my second child. And, it was not my decision, it was our decision. My wife was an equal partner, and did as much behind the scenes in making the sequencing happen.

Disruptive ages happen…and they happen fast

A friend of mine was pointing out that there is something of an anti-civilizational polemic in Against the Grain: A Deep History of the Earliest States. It’s the same sort of impulse which also asserts that “Rome never fell it evolved” and that the “Dark Ages” is a myth. I pretty much agree with Scott Alexander’s take. The datum that pollution due to lead did not match that of Classical Antiquity until the early modern period is one I remember as a searing one from The Fall of Rome: And the End of Civilization. You can’t really argue with that.

After reading The Fall of Rome I had a period when I read a lot of stuff on late antiquity. For example Peter Brown’s The Rise of Western Christendom: Triumph and Diversity, A.D. 200-1000. Brown is a serious scholar, and I’ve read several more of his books. But, I do think it shares something with earlier scholarship, and some of the more polemic recent screeds of Rodney Stark (see How the West Won), and that is that Christianity is viewed as a good in and of itself.

That is, if there is one thing that can be said for the period after the fall of Rome, it is that Christianity transcended its Mediterranean focus, and became a truly international religion, and a light unto the nations. If you believe that Christianity is true, then details about population collapse and a recession of cultural productivity matter a lot less than otherwise.

I think the economic historical evidence on the balance does lead to the conclusion that the Roman Empire achieved an optimum of economic development during the Antonine period of the 2nd century A.D. through classical efficiencies on the margin (e.g., specialization through trade, bringing all of the land into production, etc.). These levels were not again reached until after 1000 A.D. in Europe, though comparisons are not entirely apt because innovations such as the moldboard plow and windmills allowed for increases in genuine economic productivity.

The bigger question that looms in the background though is would it have been better to be a median Roman citizen or a median subject of a Dark Age warlord? I don’t have a strong opinion on this, especially when it comes to the ability to consume above subsistence.  It seems likely that the far worst treatment of slaves in places like Sicily than anything serfs were subject to (though serfdom only truly came into its own during the end of the Dark Ages) should be weighed in the calculus, but the Roman peace was also a genuine peace. The petty conflicts persistent at a local level in the Dark Ages may have made the life of a typical peasant less secure than for Roman citizens.

Rather constant reports of subjects and citizens fleeing from strong political units, or more “advanced” nations (e.g., the early American frontier), tell us something real. People valued freedom. But not everyone fled, so we’re probably seeing a bias in terms of who attempted to escape the shackles of civilization (e.g., young able-bodied single men, in particular, loom large in these reports, and I think there’s a reason for that).

Near Prehistory in Northern Europe was an Indo-European world

The Picts were the topic of discussion on this week on In Our Time. They are a mysterious yet intriguing people because we don’t know much about them in their own words, but, they are one of the roots of modern Scottish identity. When I first encountered the Picts decades ago there was some debate as to whether they were a pre-Indo-European people or not. Today that seems to not be a hypothesis people entertain. Rather, the Picts were simply the least Romanized of the Brythonic Celtic people of Britain.

Today because of the genetic data I think we can be rather confident that by the time of the Roman Empire there were no non-Indo-Europeans left in Northern Europe. The Beaker people in Britain and Ireland seem to have overwhelmingly replaced the native population of farmers, whose ancestors had predominantly arrived from the eastern Mediterranean thousands of years ago (via the Atlantic littoral or Central Europe). Across Northern Europe, in general, the replacement of the previous populations was substantial, though not total.

In Southern Europe, the arrival of Indo-Europeans was more fitful, and persistence of Basque attests to the fact that non-Indo-European languages were spoken down to historical times (if Etruscan is considered native to the Italian peninsula, that’s another example, though this is hotly debated and I lean toward the exogenous model). The pre-Latin language of Sardinia was almost certainly not Indo-European, while Greek has a high proportion of non-Indo-European words in its lexicon.