The sex ratio is in the X

k8488In The Horse, the Wheel, and Language: How Bronze-Age Riders from the Eurasian Steppes Shaped the Modern World the archaeologist David Anthony outlines the thesis that migrations from the west Eurasian steppe during the Bronze Age reshaped the culture of Northern Europe. When Anthony published the book, which you should really read if you are interested in this topic, it was a somewhat heterodox position. Though his intellectual pedigree is of long standing, arguably going back centuries, and extending down the present with J. P. Mallory’s In Search of the Indo-Europeans, in the past few decades diffusion of different sort has been paramount. In particular, the thesis that Indo-Europeans arrived with the first agriculturalists was of late ascendant, with some support being received from phylogenetic modeling of language evolution.

Anthony’s thesis in a way was a halfway house between early modern migrationism from the Eurasian steppe the newer theories. He proposes that the influence from the steppe via the Kurgan people was due to elite dominance and cultural emulation. An analogy here might be that of Hungary, where a Ugric speaking elite eventually imparted to the people a language, but very few distinct genes.

Eventually Anthony collaborated with some geneticists, and provided samples for DNA analysis. The results ended up resulting in a resurrection of migrationism, Massive migration from the steppe was a source for Indo-European languages in Europe. From what I have heard Anthony’s reaction was one of some shock as the magnitude of the genetic change.

5156rR+E2lL._SX326_BO1,204,203,200_That’s the high level view. But what about the details? Over the past few years I’ve highlighted work that indicates that many Y chromosomal lineages are star-shaped. That is, they underwent recent demographic expansion. Recent as in on the order of ~5,000 years ago in the past. But the Y chromosome is just one locus. I’ve always been curious about results from the X because the X also gives you good sex specific dynamics; 2/3 of the time it is spent in females, and 1/3 of the time in males.

Amy Goldberg has done so, Familial migration of the Neolithic contrasts massive male migration during Bronze Age in Europe inferred from ancient X chromosomes:

Dramatic events in human prehistory, such as the spread of agriculture to Europe from Anatolia and the Late Neolithic/Bronze Age (LNBA) migration from the Pontic-Caspian steppe, can be investigated using patterns of genetic variation among the people that lived in those times. In particular, studies of differing female and male demographic histories on the basis of ancient genomes can provide information about complexities of social structures and cultural interactions in prehistoric populations. We use a mechanistic admixture model to compare the sex-specifically-inherited X chromosome to the autosomes in 20 early Neolithic and 16 LNBA human remains. Contrary to previous hypotheses suggested by the patrilocality of many agricultural populations, we find no evidence of sex-biased admixture during the migration that spread farming across Europe during the early Neolithic. For later migrations from the Pontic steppe during the LNBA, however, we estimate a dramatic male bias, with ~5-14 migrating males for every migrating female. We find evidence of ongoing, primarily male, migration from the steppe to central Europe over a period of multiple generations, with a level of sex bias that excludes a pulse migration during a single generation. The contrasting patterns of sex-specific migration during these two migrations suggest a view of differing cultural histories in which the Neolithic transition was driven by mass migration of both males and females in roughly equal numbers, perhaps whole families, whereas the later Bronze Age migration and cultural shift were instead driven by male migration, potentially connected to new technology and conquest.

Screenshot 2016-09-30 22.33.39The figure to the left shows the inferences made in regards to the quantitative contribution of farmer males and females, and steppe males and females, to Bronze Age European populations. In short, it looks like the population of Northern Europe derives from a fusion of males from the steppe, and native females, who themselves arose out of a group of peoples which synthesized the ancestry of European hunter-gatherers and West Asian farmers.

But one of the more interesting things about this preprint is that the admixture can’t be modeled by a single pulse event. It seems that there were repeated migrations out of the steppe over multiple generations. But, these men did not bring women, at least in large numbers. The preprint lays out the common sense reason: these were mobile groups, probably bands of men with weapons. If your game is predation on other humans, having a baggage train of women and children is not optimal.

There is a historical analog to what might have happened. Argentina is a nation where mitochondrial lineages show a lot of Amerindian heritage. But the whole genome far less. This is because of male biased migration from Europe. One generation of this would result in a mixed population, but many generations would slowly replace the whole genome.

We will never know in concrete terms what social-political organizations the Indo-Europeans set up once they conquered the plains of Northern Europe, because we don’t have writing. But it seems unlikely that we’re talking about only band or clan level scales of organization. Rather, it was likely that a ‘Indo-European commonwealth’ of some sort existed initially, predicated on domination and extraction of value from the natives. In such a fashion one can imagine Europe being a draw for enterprising males from the steppe. This could also explain likely ‘back migration’ over time, leading to ‘European’ ancestry among later steppe cultures.

Scale of time and space in admixture

Screenshot 2016-09-30 08.23.21As you may know in Britain there is a new direct to consumer genetic testing service, Living DNA. Debbie Kennett has a post up where she talks about how it works and why it’s different. For now it is British focused, and leverages haplotype-based methods with the PoBI database to give really fine-grained analysis to their customers on those sceptered isles.

Brought to you by the same people who brought you FineStructure, this is a major offering in this space.

But there’s a more general issue I want to comment on. In the video accompanying the website, one of the presenters states that people are “very surprised how admixed” humans are. This depends on scale.

Let’s start at a time, 0. In the short term you are not very admixed usually. Outside of the Americans and other settler societies admixture is not common on the scale of recent generations. But as you go further back, you become quite admixed. E.g., The Geography of Recent Genetic Ancestry across Europe showed lots of admixture on 1,000 year scales within Europe. David Reich’s lab has shown lots of admixture between very diverged populations on a 5,000 year scale. But as you go further back the ‘admixture’ gets lower and lower, and at some point you hit the species barrier, and you see the same genealogies coalescing again and again through the bottleneck.

Now, look at space. As distance is ~0 you’ll see lots of admixture. But as you push further and further away, the admixture drops. At some point the admixture is quite boring. Ergo, all the “you are 100% European” results from DTC companies.

The two dimensions look quite different. Admixture increases as you go further back in time…until it doesn’t. You’re hitting the “species” taxonomical barrier. In terms of space, admixture decreases the further you go away from your focal point of interest.

Open Thread, 9/25/2016

4197TkGD1DL._SY344_BO1,204,203,200_At a readers’ suggestion I got Explaining Postmodernism: Skepticism and Socialism from Rousseau to Foucault. Unlike The Dialectical Imagination this is not necessarily a detached academic book. Rather, the author has a definite perspective. About 20 years ago I read George H. Smith’s Atheism: The Case Against God, and there are a lot of similarities between the two books. From that I suspected before doing some research that the author had some influence from Objectivism, and that seems correct. I don’t care too much, and I probably broadly share the authors’ libertarian/classical liberal politics, but the middle sections of the Explaining Postmodernism got a little preachy for my taste.

Nevertheless the first half especially is excellent, and it outlines a genealogy of the Postmodern movement very concisely and in an illuminating manner. There are some details where one might quibble (e.g., the relationship of Immanuel Kant to religion is much more in dispute than presented in Explaining Postmodernism, though that’s a minor objection). But the progression of Transcendental Realism down to the morass we see around us today is a familiar story told more crisply here then elsewhere.

The author does outline a sociological origin for Postmodernism which is very intriguing, as it explains why it is an overwhelmingly far Left movement, despite the implications toward extreme relativism and subjectivism one might infer from the worldview. But there is something that is omitted here, perhaps because the author was not aware of this fact: there is a relationship of Postmodernism to elite intellectual religious revival in the past few decades.

418lqzfRjwL._SY344_BO1,204,203,200_Alister McGrath is a proponent of this school, and outlines his thesis in The Twilight of Atheism: The Rise and Fall of Disbelief in the Modern World. To condense McGrath’s argument, if everything is a superstition, then people will fall back on the tried and true superstitions. McGrath asserts the collapse of the authority of rationality and philosophical realism signal the end of the Enlightenment project, and undermines the secular world. As an empirical matter there is a lot one can quibble with here; in particular, though Postmodernism may be vigorous in the academy, science and technology are concrete witness to power of naive realism and rationalist presuppositions. But McGrath’s position is philosophically cogent. And, it is not well known, but the doyen of modern Intelligent Design, Phillip E. Johnson, has admitted that the he was strongly shaped by Critical Theory:

I used to refer jokingly to myself as the entire right wing of the Critical Legal Studies movement, which in their view was a contradiction in terms. Their critique was purely the instrument of a left-wing political program, which was chosen arbitrarily and presumed to be good. It was a faith commitment.

So I’m reading a lot of things on Postmodernism. I’m going back to Hegel. On the one hand this is a major opportunity cost. There’s a lot of science and programming stuff I want to read that I don’t have time to read. On other hand, much that I was suspecting becomes very clear. Ultimately I’m respecting Postmodernism more insofar as it is a reasonable tool from what I can see in destroying certainty and realism for those who are innumerate. If you have any understanding of statistics you’re pretty insulated from Postmodernism. But very few people think statistically. I also now believe it is ultimately far more dangerous than before, because it is a serious intellectual tool that can deconstruct much that is precious and rare in the world. In particular, the Enlightenment project, which in many ways goes against the world historical grain, or at least the grain of human intuitions and preferences. Postmodernism as an intellectual exercise is easy to dismiss. But as a tool of political battle it has to be taken seriously.

A Single Migration From Africa Populated the World, Studies Find. I will blog these papers. It’s a question of time. Please don’t pester me on non-open threads about this stuff.

Widespread allelic heterogeneity in complex traits.

14390818_10153997292567984_5603508903928344619_nGunman kills Jordanian Christian writer charged over anti-Islam cartoon. The title is misleading, as the cartoon was making fun of jihadists, not Islam. He posted the cartoon on Facebook.

Chinese Jews of Ancient Lineage Huddle Under Pressure. Most of the Kaifeng Jewish community was absorbed into the Han, though some became Muslim.

Academic Research in the 21st Century: Maintaining Scientific Integrity in a Climate of Perverse Incentives and Hypercompetition.

Please use the “open thread” for random stuff. The OT comments early in threads are pretty annoying.

Also, if you follow me on Twitter if you tweet at me a lot, and I don’t respond, but you keep tweeting at me demanding a response, I’m probably going to block you. Also, I get annoyed at readers and Twitter followers who presume they know my state of mind or aspects of my life from what they see on the interwebs. If you do that and tweet at me, I’m going to block you, just as if you do that in the comments here your chances of me publishing future comments goes way lower. If you have read me for a while you should be aware that I have a really long memory and recall commenters who have crossed me in some way for years, so even if I let you comment again please don’t think I’ve forgotten. The major problem is commenters who presume over-familiarity with me. Probably a function of the low social intelligence of many of my readers.

Finally, Sean don’t post anything on sexual selection on this thread. I won’t post the comments.

The future as it appeared in the 1980s


Airports are in interesting window into architecture and perceptions of the future. When I landed at Vienna International in 2010 it was as if I landed back in the 1970s. In contrast, Frankfurt Airport was the closest I’ve felt to really be pushed into the “gleaming future” you sometimes see in science-fiction films.

With that in mind, lately I’ve been thinking that for some reason the airport at Detroit reminds me of what the future was going to be like in my childhood of the 1980s.

The sequenced generation


There was a time, five years ago or so, when we knew all the humans who had been sequenced. Or at least most of them. But now we’re coming into the period when the first sequenced animals of any given species are starting to die. Above is Cinnamon, the first sequenced cat is no longer with us. And some day the hour will come when Craig Venter, who was a major contributor to the first human genome, will no longer be with us.

Something to consider.

Vlogging human evolutionary genomics

The Estonian Biocentre has been one of the best resources in human population genomics, because their policy under Mait Metspalu seems to be to release the data once it’s published. Today I went and checked the site, and noticed a vlog accompanying their Nature paper, Genomic analyses inform on migration events during the peopling of Eurasia.

Well done.

The cats came, they conquered, and they purred


I don’t mean to be an Ewen Callaway clipping service (though there are worse things to be), but today he has a piece up on ancient feline DNA and what it might imply for the distribution and spread of cats, How cats conquered the world (and a few Viking ships). My dissertation project is no longer on felines, but I spent several years doing analysis and thinking deeply on the issue of how cats emerged, and what might account for their contemporary distribution and phylogeographic relationships.

There are a few things I can divulge without scooping any future researchers who might work the data I’ve seen. First, ships and cats seem to be very closely connected. That is, maritime trade routes turn out to be highly suggestive of many of the patterns you see. This goes to the distinction between cats and dogs: the former are definitely creatures whose coexistence with humanity is conditional on complex civilization. The “finer things” in life, as it were.

The “domestication” of the cat is probably hard to disentangle from the emergence of urban centers, and the vermin which they attracted. What humans term vermin, the cats would naturally consider prey. The selective pressures are easy to imagine. Cats and humans are now companions, but initially their interests were simply concurrent.

And just as cities emerged independently in several locales (as well as agriculture), it is not implausible that domestic felines emerged from different wild populations, though at this point I’m modestly skeptical of most claims. Though it is not unlikely that there is introgression or admixture from diverged wild lineages into many domestic cat populations, the evidence of independent domestications is weak in my judgment. In contrast, cattle seem to be derived from two very distinct groups.

Rather, these research point to deep ancient structure among Middle Eastern feline groups, and parallel possibilities of human-cat coexistence as farming communities emerged rapidly during the early Holocene, with exigencies of historical events leading to later phylogeographic patterns we see around. I think the above research is on the right path. There is definitely a connection between most European domestic cat lineages and the indigenous populations for Egyptian cat (for example).

The dead weight of culture

Screenshot 2016-09-19 02.06.35The map to the right shows GDP per capita in the European Union in 2014 broken down by regions. I’ve long observed that the wealthiest regions of Europe are disproportionately those which were long under Habsburg rule. This fact transcends ethnicity and religion. Catholic northern Italy, Catholic southern Germany, as well as Protestant Netherlands, are all notably economically productive, and were long under Habsburg rule or hegemony.

The observation is just that, an observation. I have no grand theory to explain what is going on. And some have suggested that the outlines of this productive zone of Europe might even go back as far as Lotharingia. But, these sorts of patterns rooted in geopolitical history might hint at the possibility that cultural norms and institutions can be deeply rooted in region and locale.

This is at variance with our intuition that culture is protean and can change rapidly. This is most easily illustrated by the shift from militarism to pacific evident in both Japan and Germany in the past few generations. A shift that most believe could reverse course in short order.

In a similar vein, Peter Turchin has a post up at his blog, Ghost of Empires Past, which shows how pre-modern political structures continue to live in patterns in the World Values Survey!

Admixture analysis isn’t wrong, it misleads

Screenshot 2016-09-18 20.57.52

The above results are from Ancestry. You can see here 4% Melanesian. This is common in South Asians. And it’s not an error in the method. Rather, it is a natural outcome of the methods uses to generate admixture profiles.

Basically what’s going on is this:

1) You have data. In this case, the data are your own genotypes, as well as that of a set of individuals which represent world genetic variation, and are categorized into discrete populations.

2) You have a model or set of models. These models have different parameters.

3) You look at the data you have, and pick the parameters which best explain the data given the model.

If you have 100,000 or more markers that’s more than enough genotype data for individuals. The models themselves are quite stylized (e.g., HWE random mating sets of populations), but close enough to reality to give good results in many cases. For example, Ashkenazi Jews are often assigned to be ~100% Ashkenazi Jewish through these methods.

Then again, Ashkenazi Jews are a good test case. This is a population which went through a bottleneck about 500 to 1,000 years ago, and has been reasonably endogamous most of this time. Additionally, it’s not extremely structured due to inbreeding in different clan lineages. Though cousin marriage and uncle-niece marriage has been practiced by Ashkenazi Jews, the runs of homozygosity you see in Jewish genomes is not such that indicates a highly inbred population, as is common in the Middle East or South Asia. Rather, there are lots of medium length segments identical by descent across individuals.

Ashkenazi Jewish population is rather simple, and it is actually a rather clear and distinct population cluster. It stands to reason that when you create an Ashkenazi Jewish reference panel in your training data set it’s a pretty good match to the individuals you are testing.

The problems occur when you are to generate clusters and ancestry assignments for populations which are not so clear and distinct. Why do South Asians routinely come out as part Melanesian or Polynesian? This post was prompted by a Facebook thread where a South Asian customer of Ancestry was interested to see she had Polynesian ancestry. The reality is she almost certainly does not have Polynesian ancestry.

What’s going on is that the reference panel for South Asians used by many of the DTC genomics companies is not diverse enough to capture South Asian genetic diversity. There is an element of South Asian ancestry, “Ancestral South Indian” or ASI, which has deep shared ancestry with populations across Southern Eurasia and out toward Oceania. The admixture analysis method is searching through the reference panels for combinations of genotypes which can explain individual genetic variation. Since the South Asian training set is insufficient to explain all the South Asian variation the algorithms are filling in the balance of the variation with the closest available proxies to the “ghost clusters.”

The method is constrained and conditioned on two things:

1) The data being put in, which is often insufficient.

2) The set of populations that it is forced to work with to generate the combinations in individuals (the parameter values in the model to explain the data) are often insufficient or artificial.

What I mean by the last is that many of the genetic clusters are not taxonomically equivalent. “South Asian” ancestry is much more diverse and diffuse than “Melanesian” ancestry. This why Melanesian ancestry can explain South Asian ancestry, but generally not the reverse.