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

May 31, 2018

Dallas area teen wins National Spelling Bee

Filed under: Culture,Spelling Bee — Razib Khan @ 6:55 pm
Congratulations Karthik!

Though Texas doesn’t get all the glory! The National Geo Bee was won by a kid from Northern California.

Congratulations Venkat!

May 30, 2018

The cultural conditions of star-shaped phylogenies

Filed under: Population History,Y chromosomal lineages — Razib Khan @ 11:53 pm

In the generality, I think intergroup selection of paternal lineages is the answer to why star-shaped phylogenies are so evident in the phylogenetic record ~4,000 years ago. More precisely, most of the major clades of R1a, R1b, and I1 undergo massive expansion after a sharp reduction in effective population size around this period. The R lineages diversified during the Pleistocene, probably in Central Eurasia (it is a brother clade to Q). The I lineage derives from Western European hunter-gatherers, probably the late Pleistocene expansion which eventually gave rise to the Mesolithic groups that encountered the early farmers.

But what happened here specifically? Let me quote a section of Peter Turchin’s excellet Ultrasociety: How 10,000 Years of War Made Humans the Greatest Cooperators on Earth:

Lanchester’s Square Law yields an enormous return to social scale. If the opposing forces use a mix of ranged and shock weapons, numerical superiority will still be amplified, although not as much as with purely projectile weapons. So there is an intense selection pressure for cultural groups living in flat terrain to scale up, and a very high price to pay by those that fail to do s….

Though human interaction with horses as domesticates is probably older, light chariots emerged on the Pontic steppe ~4,000 years ago. Within a few centuries, this technology was ubiquitous in the Near East. The Indo-Aryan Mitanni arrive with chariots in modern Syria/Northern Iraq by ~3,750 years ago.

In the Near East chariots and bows were closely associated. The evidence from the Eurasian steppe during the Bronze Age seems less definitive (simply, bows may not preserve very well), though by the Iron Age the mounted archer became a ubiquitous feature of the military landscape.

The combination of chariots, likely bows, and the Sintashta/Srubna/Andronovo culture’s known focus on metallurgy, make it hard for me to deny the likelihood that the expansion of R1a1a-Z93 has something to do with intergroup conflict. The reality is that Lanchester’s Square Law means that even small initial advantageousness for a given paternal lineage will probably snowball. One victory will lead to an increase in territory and resources, which will produce later advantage. A sort of Y chromosomal Matthew Effect.

But this doesn’t explain what occurred in Europe, where R1b and I1 also underwent a massive expansion (and R1a as well). Europe’s relatively forested territory beyond the Hungarian plain always blunted the power and reach of mounted archers later in history. We do know that chariots arrived in the Mediterranean around the same time as in the Near East. But the rise to dominance of the Corded Ware and Bell Beaker peoples predates light chariots. Perhaps it is something as simple as the fact that metaethnic institutions and identities that could dampen intergroup conflict hadn’t emerged, but it’s still curious to me that one could have a ~90% population replacement in Britain in a few centuries.

Perhaps we will find out that it has to do with a disease as our understanding of ancient epidemics gets better.

 

The once and future “Brown Pundits”

Filed under: Blog,Brown Pundits — Razib Khan @ 4:18 pm
Country Users Rank % Rank
 China 746,662,194 1 53.20% 109
 India 391,292,631 2 29.55% 143
 United States 245,436,423 3 76.18% 54
 Brazil 123,927,230 4 59.68% 90
 Japan 117,528,631 5 92.00% 15
 Russia 110,003,284 6 76.41% 53

The “Brown Pundits” blog was formed on a lark about 7 years ago. The Sepia Munity weblog was clearly winding down, and people like Zach and I didn’t feel too well represented. What I mean is that weblog in its latter years reflected a certain activist Left-wing South Asian American perspective which naturally didn’t include all Diaspora South Asians. In some ways this was a shift away from its original years, when it was more politically eclectic, with some center-Right and libertarian voices, to go along with conventional center-Left viewpoints.

Two of the co-founders I knew personally before the blog was founded, and we had a small e-list where we discussed cultural and social issues. To a great extent, I think the Sepia Mutiny blog reflected a decade in transition for South Asian brown Americans. Most of the contributors were of an age where they would be routinely asked where “they were really from,” and all of us understood that we were seen to be a novel and exotic contribution to the American landscape.

Things have changed a lot since then. Most particularly in 2008, Barack Hussein Obama was elected president of the United States. Where black Americans rejoined in the election of a black man, I suspect many Americans of Asian background noted his exotic background and name. If a man with such a foreign name could become head of state of the United States could we be such aliens after all?

I do understand that some people feel that the election of Donald J. Trump has rendered us aliens in our own land again. Overall, I disagree. In a Spenglerian sense, I see the election of Trump as a crying in the wilderness of an old America which is feeling less at the center of our culture, as well as the more general atavisms triggered by globalization.

South Asian Americans, which mostly means Indian Americans, have a place and a role in American culture that can’t be denied. Most Indian Americans have followed a “Jewish model”, aligning with the political and social Left, especially a small activist class.

A framework to understand the trajectory of young 2nd and later generation South Asian Americans that I outlined over 10 years ago I think is a useful model. Roughly, there are three broad classes of South Asian Americans (with overlap):

  • Assimilators. Unlike some groups, South Asian Americans are physically distinct enough that assimilation doesn’t involve “passing” into another identity. Rather, assimilation involves intermarriage and socialization with a broad set of Americans and a very loose attachment to distinctively South Asian cultural markers ad community institutions. Most of the children of assimilators will be mixed, and so will not have a singular South Asian identity in an authentic way.
  • South Asian Americans. This group is perhaps equivalent to Indian identities in the West Indies, which have become distinct from Old World self-conceptions while retaining a sense of South Asianness. In some ways, I think this was a core group for the Sepia Mutiny blog. These are the sort of people who might marry other Indian Americans, but these marriages are often cross-regional, cross-caste, and even cross-religion. To give a concrete example, I know that two of the original Sepia Mutiny bloggers married and had children with someone whose family was from a different ethnoreligious tradition from their own. The sort of marriage which would raise eyebrows in South Asia, but wouldn’t be viewed that strange in the American context.
  • Finally, traditionalists. There are American-born and raised Patels who marry other Patels. There are Dawoodi Bohra Muslims who marry other Dawoodi Bohra Muslims. This group would be most recognizable to people from South Asia.

But to me, that’s the past. I think it’s done. I don’t see Brown Pundits contributing to that discussion or cultural space, for various reasons (the primary one being most that none of the contributors are of the second class). Rather, I’ve started to get interested in Brown Pundits in large part because it seems that Asia, including South Asia, is getting to be a bigger and bigger part of the discussion. There are now more Indians browsing the internet than Americans!

Yes, it’s mostly on mobile phones, but most Americans were on dial-up until the mid-2000s.

Soft & hard selection vs. soft & hard sweeps

Filed under: Population genetics,Quantitative Genetics — Razib Khan @ 12:09 am


When I was talking to Matt Hahn I made a pretty stupid semantic flub, confusing “soft selection” with “soft sweeps.” Matt pointed out that soft/hard selection were terms more appropriate to quantitative genetics rather than population genomics. His viewpoint is defensible, though going back into the literature on soft/selection, e.g., Soft and hard selection revisited, the main thinkers pushing the idea were population geneticists who were also considering ecological questions.*

The strange thing is that I had already known the definitions of hard and soft selection on some level because I had read about them as I was getting confused with hard and soft sweeps! But this was more than ten years ago now, and since then I haven’t given the matter enough thought obviously, as I defaulted back to confusing the two classes of terms, just as I used to.

Matt pointed out that truncation selection is a form of hard selection. All individuals below (or above) a certain phenotype value have a fitness of zero, as they don’t reproduce. In a single locus context, hard selection would involve deleterious lethal alleles, whose impact on the genotype was the same irrespective of ecological context. So in a hard selection, it operates by reducing the fitness of individuals/genotypes to zero.

For soft selection, context matters much more, and you would focus more on relative fitness differences across individuals/genotypes. Some definitions of soft vs. hard selection emphasize that in the former case fitness is defined relative to the local ecological patch, while the latter is a universal estimate. Soft selection does not necessarily operate through the zero fitness value for a genotype, but rather differential fitness. Hard selection can crash your population size. Soft selection does not necessarily do that.

Though I won’t outline the details, one of the originators of the soft/hard selection concept analogized them to density-dependent/independent dynamics in ecology. If you know the ecological models, the correspondence probably is obvious to you.

As for hard and soft sweeps, these are particular terms of relevance to genomics, because genome-wide data has allowed for their detection through the impact they have on the variation in the genome. A “sweep” is a strong selective event that tends to sweep away variation around the focus of selection. A hard sweep begins with a single mutant, and positive selection tends to drive it toward fixation.

A classical example is lactase persistence in Northern Europeans and Northwest South Asians (e.g., Punjabis). The mutation in the LCT gene is the same across a huge swath of Eurasia. And, the region around the genome is also the same, because regions of the genome adjacent to that single mutation increased in frequency as well (they “hitchhiked”). This produces a genetic block of highly reduced diversity since the hard selective sweep increases the frequency of so many variants which are associated with the advantageous one, and may drive to extinction most other competitive variants.

Someone is free to correct me in the comments, but it strikes me that many hard selective sweeps are driven by soft selection. Fitness differentials between those with the advantageous alleles and those without it are not so extreme, and obviously context dependent, even in cases of hard sweeps on a single locus.

The key to understanding soft sweeps is that there isn’t a focus on a singular mutation. Rather, selection can target multiple mutations, which may have the same genetic position, but be embedded within different original gene copies. In fact, soft selection often operates on standing variation, preexistent alleles which were segregating in the population at low frequencies or were totally neutral. Genetic signatures of these events are less striking than those for hard sweeps because there is far less diminishment of diversity, since it’s not the increase in the frequency of a singular mutation and the hitchhiking of its associated flanking genomic region.

Soft sweeps can clearly occur with soft selection. But truncation selection can occur on polygenic traits, so depending on the architecture of the trait (i.e., effect size distribution across the loci) one can imagine them associated with hard selection as well.

Going back to the conversation I had with Matt the reason semantics is important is that terms in population genetics are informationally rich, and lead you down a rabbit-hole of inferences. If population genetics is a toolkit for decomposing reality, then you need to have your tools well categorized and organized. On occasion it is important to rectify the names.

* There are two somewhat related definitions of soft/hard selection. I’ll follow Wallace’s original line here, though I’m not sure they differ that much.

May 29, 2018

Brown Pundits 2018 Reader Survey

Filed under: Blog,Survey — Razib Khan @ 5:38 pm

I created a SurveyMonkey poll. Check it out….

(after you are done, you can check out the results)

Create your own user feedback survey

May 28, 2018

Open Thread, 05/28/2018

Filed under: Open Thread — Razib Khan @ 11:45 pm

She Has Her Mother’s Laugh is now available. The interview with Carl Zimmer will be live on The Insight Wednesday night (EDT).

If you haven’t, please consider leaving a 5-star review on iTunes or Stitcher.

I’ve told that you can already read The University We Need on Google Books. I can’t vouch for this, but on Amazon the publication date is July 10th.

I suspect the field of cultural evolution is going to become big in the next ten years, breaking out its relatively rarified ghetto. If you haven’t, I’d recommend The Secret of Our Success by Joe Henrich.

The older, more technical books, are Cultural Transmission and Evolution, Culture and the Evolutionary Process.

I noticed the other day that the spam filter was a little overactive recently. Just in case you notice comments not going through….

May 26, 2018

Y chromosomal star-phylogenies as inter-group competition between paternal lineages

Filed under: Human Population Genetics,Star phylogenies,Y chromosomal lineages — Razib Khan @ 11:37 pm

The figure to the left should be familiar to readers of this weblog. It is taken from A recent bottleneck of Y chromosome diversity coincides with a global change in culture (Kamin et al.). Over the past few years a peculiar fact long suspected or inferred has come into sharp focus: some of the Y chromosome haplogroups very common today were not so common in the past, and their frequency changed very rapidly over a short time period.

What Kamin et al. did was look at sequence data across the Y chromosome to make deeper inferences. The issue is that the Y chromosome is not genetically very diverse. Earlier generations of researchers focused on highly mutable microsatellite regions for identification. While microsatellites are good for identification and classification because of their genetic diversity, they are not as good when it comes to making evolutionary inferences about parameters such as time since last common ancestor. They have very high and variable mutation rates.

Single nucleotide polymorphisms (SNPs) are probably better for a lot of evolutionary inference, but the Y chromosome doesn’t have too many of these. SNP-chip era technology which focuses on a select subset of polymorphisms at specific locations didn’t have much to choose from and likely missed rare variants.

This is where whole-genome sequence of the Y comes in. It retrieves maximal information, and with that, the authors of Kamin et al. could definitely confirm that some Y chromosomal lineages under explosive expansion ~4,000 years ago after a bottleneck.

By and large ancient DNA take a different angle, focusing on genome-wide autosomal ancestry, and lacking in high-coverage whole-genome sequences. But they have confirmed the inferences from whole-genomes that some of these lineages exhibit explosive growth in the last ~4,000 years. One moment they were rare, and the next moment ubiquitous.

But geneticists are geneticists. They’re interested in genetical questions, methods, and dynamics. To be frank cultural models for how those genetic patterns might have come about are either exceedingly simple and probably true (e.g., gene-culture coevolution with lactase persistence), or vague and handwavy. With the surfeit of genomic data to analyze it isn’t surprising that this happens.

This is why researchers in the field of cultural evolution need to get involved. They’re model-builders and should see which models predict the copious empirical results we have now when it comes to genetic change over time.

For several years now I have been asserting that inter-group competition of paternal lineages best explains the pattern of Y chromosome expansions ~4,000 years ago. A new paper brings forth a formal model which explores this hypothesis, Cultural hitchhiking and competition between patrilineal kin groups explain the post-Neolithic Y-chromosome bottleneck:

In human populations, changes in genetic variation are driven not only by genetic processes, but can also arise from cultural or social changes. An abrupt population bottleneck specific to human males has been inferred across several Old World (Africa, Europe, Asia) populations 5000–7000 BP. Here, bringing together anthropological theory, recent population genomic studies and mathematical models, we propose a sociocultural hypothesis, involving the formation of patrilineal kin groups and intergroup competition among these groups. Our analysis shows that this sociocultural hypothesis can explain the inference of a population bottleneck. We also show that our hypothesis is consistent with current findings from the archaeogenetics of Old World Eurasia, and is important for conceptions of cultural and social evolution in prehistory.

Their model is interesting because inter-group competition between paternal lineages can result in a loss of haplogroup diversity without huge reproductive skew. That is, instead of a highly polygynous society, one can simply posit that group dynamics of expansion and extinction produce expansions of Y chromosomal lineages.

A formal model synthesized with genomic results is a major step forward, though I haven’t dug into the methods (computational or analytic). Presumably, this is a first step.

But the discussion does review a lot of anthropological literature about the nature of human conflict and social interaction. Basically, it seems that between nomadic hunter-gatherers and before chiefdoms, biologically defined paternal clans were often the organizing principle of society. To some extent this makes total sense since the meta-ethnic religious and social identities explicitly appeal to fictive relationships of blood even after blood was no longer paramount. Ancient Near Eastern kings addressed each other in familial terms (e.g., “brother” and “son”), while universal religions deploy the construct of brotherhood.

In Empires of the Silk Road the author makes the case that these bands of brothers were more influential in shaping history than we realize today. Not surprisingly, the authors of the above paper suggest that the Inner Asian nomad zone is where star-phylogenies have been most pervasive and persist down to historical time. As in Steven Pinker’s The Better Angels of Our Nature it seems that the rise of the state suppressed the viciousness of the paternal kin group. How do we know this? Because the period of the maximal explosion of star-phylogenies seem to be a transient between the early Neolithic and the historical age.

The Y chromosomal literature is just the low hanging fruit. I suspect in the next decade cultural evolutionary models will be brought to bear on the huge mountain of genomic data….

Citation: Cultural hitchhiking and competition between patrilineal kin groups explain the post-Neolithic Y-chromosome bottleneck Tian Chen Zeng, Alan J. Aw & Marcus W. Feldman.

Books on Indian history without recency bias

Filed under: History — Razib Khan @ 3:17 pm

One of the problems with Indian history is that a lot of the books are strongly biased toward the Muslim and colonial periods. There are numerous reasons for this. People are interested in the Muslim and colonial periods for nationalist and anti-nationalist reasons, if that makes any sense.

But some of it is simply source availability of. When I am curious about the period between the Han dynasty and the Sui-Tang I’ll pick up a book like China between Empires: The Northern and Southern Dynasties. In contrast The Gupta Empire is an out of print monograph.

Because at some point the Rakhigarhi DNA results will be coming out I want to do some more reading on ancient and medieval (using those epochs loosely in the South Asian context) history, but so much of it is archaeological because of the thin historiographical tradition in South Asia.

Do readers have suggestions?

(Please calibrate to my level of knowledge. I’ve already read Early India)

May 25, 2018

Arise the coalescent!

Filed under: Biology,Evolution,Genetics,science — Razib Khan @ 12:14 pm
Citation: Modeling Human Population Separation History Using Physically Phased Genomes

Evolution is sometimes difficult to comprehend in terms of how it plays out in your mind’s eye. This is different from believing that evolution occurred. Evolutionary ideas were in the air when Charles Darwin and Alfred Russell Wallace both developed a theory of morphological change and speciation driven by adaptation in the middle of the 19th century. Their genius was introducing natural selection as the motive force underlying the change. But both of these thinkers lacked a true mechanism of heredity, so the formal extension of the field was hobbled.

With the emergence of genetics in the years after 1900, evolutionary science developed into a new and powerful form, what we now call the “Neo-Darwinian Synthesis.” This project combined the descriptive richness of natural history, the explanatory power of classical conceptual Darwinism, and the formal precision of population genetics.

The Neo-Darwinian Synthesis rests to a great extent on population genetic models. The most elementary of those models is that of the Hardy-Weinberg Equilibrium (HWE) — a large random mating population not subject to selection or drift. Deviations from the conditions of these models allow us understand the processes that are occurring in specific populations.

In the lab, researchers use matings between organisms such as Drosophila that deviate from the assumptions underneath the models, and see what the outcomes are. Scientists mate together flies with similar or dissimilar traits, violating random mating. They select individuals based on their characteristics, or collapse reproductive pedigrees down to a family lineage to explore inbreeding, introducing selection and random genetic drift.

But laboratory research can be both time intensive and tedious. With the rise of powerful computing tools in the last half of the 20th century scientists realized that they could simulate outcomes of their models. Just like in an experiment, researchers could change the conditions, the parameters, and see the results to the final outcome!

State of the art simulator, 1985

In the beginning, the power of simulations and computing seemed almost magical to researchers. No more time intensive sampling in the field, or expensive construction of laboratory facilities.

But over time, they began to realize that simulations also have their limitations. Computer memory and disk space costs money too, and scientists quickly found that the law of scarcity was not abolished. They couldn’t explore infinite possibilities because infinite took forever, even in a computer.

Imagine that you start with a few hundred individuals and simulate them randomly “mating.” You stipulate that their population grows 2% every generation. After a 100 generations, your population size is 10 times larger. The possible number of “mates” in your program is now 10 times greater, and there are so many more possible interactions. Anyone who has tried to work with large files knows that computing resources are finite, and simulations running forward in time run into the limits of that finitude soon enough.

But what if you moved back in time? Imagine you began with 10,000 individuals, and traced the ancestors of these 10,000 back across the generations. Genealogies can be complicated. But consider a single gene copy in your body, and compare it to another copy in another person. At some point in the distant past, the two copies share a common ancestor — they coalesce.

The coalescent sounds science fictional, but really it’s just a way to work backward from the genetic data you have now, to the past. You can create a tree of relationships back into the distant past, reversing direction with a genetic time machine. And the beauty of the coalescent from the perspective of 2018 is that computationally it is much more feasible to work back in time. With each step, you have fewer and fewer branches in the genealogy to model — back to a single common ancestor.

Instead of being overwhelmed by computational tasks, the coalescent converges upon the elegant simplicity of the last common ancestor, bring together late 20th century mathematics, 21st century computing, and the original conceptual insight of Darwin and Wallace of common descent.

Explore your Regional Ancestry story today.


Arise the coalescent! was originally published in Insitome on Medium, where people are continuing the conversation by highlighting and responding to this story.

May 24, 2018

The souls of peoples gone

Filed under: Demographics,Pots not Peoples,Roman History,rome — Razib Khan @ 11:14 pm



Stonehenge was first erected around 3100 BC, though the timber was only replaced with stone in 2600 BC. The great monument was a product of the Late Neolithic in Britain. Ancient DNA today tells us that these people were distantly related to the modern Sardinians, and derive from a wave of farmers that radiated out of Anatolia across much of Europe.

About a century after the stone form of Stonehenge was erected, prehistoric Britain was culturally and genetically transformed. In the space of a few centuries after 2500 BC there was nearly a ~90% genetic turnover, and a new people more closely related to Northern Europeans in Germany and further east became ascendant. The majority of the ancestry in Britain today probably derives from this migration period.

And yet the new people continued to utilize Stonehenge for over 1,000 years. Clearly, they co-opted a monument erected by their predecessors and maintained its significance across an enormous cultural disruption.

This is on my mind because on the episode of The Insight recorded with Patrick Wyman (it will probably drop in June) we talked extensively about Roman demography. And one of the peculiarities of 2013’s The Geography of Recent Genetic Ancestry across Europe is that Italy has a lot of deep population structure. From the paper:

There is relatively little common ancestry shared between the Italian peninsula and other locations, and what there is seems to derive mostly from longer ago than 2,500 ya. An exception is that Italy and the neighboring Balkan populations share small but significant numbers of common ancestors in the last 1,500 years, as seen in Figures S16 and S17. The rate of genetic common ancestry between pairs of Italian individuals seems to have been fairly constant for the past 2,500 years, which combined with significant structure within Italy suggests a constant exchange of migrants between coherent subpopulations.

The implication here is that there’s population structure deeper than the Roman period. When I first saw these results I was surprised. Looking at genome-wide data I was pretty sure that most of the modern Italian population dated to the Roman Republican period, but I was not expecting provincial level substructure. It was like telling me that the Samnites and Umbrians were still with us!

But what about the great cosmopolitan cities of Neopolis, Rome, and Ravenna? Some commenters on this blog routinely get frustrated when I dismiss the textual and epigraphic evidence of massive migration into the Italian peninsula during the height of the Roman Empire. Actually, I believe that this migration occurred. I just do not believe it was particularly impactful genetically today. Though my general outlook on this issue goes back over ten years (in part thanks to the suggestion of Greg Cochran), I believe the issue here is that cities are such incredible demographic sinks.

Roman urban cosmopolitanism was parasitic on migration. Demographically it was never self-sustaining. In fact, as Patrick points out urban areas probably did not see sustained above replacement reproduction anywhere in the world before about 1900, with the emergence of germ theory and massive public sanitation works, especially in the United States. This is evident in books as diverse as Kyle Harper’s The Fate of Rome and The Rise and Fall of American Growth.

So did Roman urban civilization leave nothing to posterity? On the contrary. Like much of Rodney Stark’s work in the last twenty years Cities of God is needlessly polemical and oftentimes unscholarly*, it gets at the reality that Christianity was fundamentally an urban cult. It was brought to Italy by people from the Eastern Mediterranean, Jews and Greeks. In its early period it was dominated by urban cosmopolitans. Some of the sermons in urban churches even castigated rural peasants  as pagan beasts of the field.

Christianity was an international religion with foreign origins, and like many elite cultural constructions of the pre-modern oikoumene its existed operationally as a social network across the various cities around which elites congregated. In some ways the vast sea of villages which filled in the landscape were untouched by many of the cultural innovations occurring in the cities. A Neolithic person might be confused by some aspects of Roman village life (in particular, access to standardized manufactured goods), but they would be totally flabbergasted by the city of Rome.

Over the 200 years between 400 AD and 600 AD the population of Rome probably went from ~500,000 to ~50,000. The decline of the Western Empire and the period of the Gothic Wars choked off the economic subsidies which could maintain the city’s population by drawing newcomers. And yet the Bishop of Rome, the Pope, remained in the city. If Patrick and I are correct then medieval Rome was repopulated by the descendants of peasants from Lazio, the hinterlands around the city.

Some scholars, albeit often from a partisan Protestant viewpoint, have suggested that the Western Christian Church of the early Middle Ages did not truly Christianize the peasantry. Whether this is true or not, it does seem to correct to say that deeply rooted popular Christianity took many centuries to become pervasive in rural areas. Despite their relative decline in the medieval period, both substantively and in terms of cultural prestige, cities remained remained the stalwart redoubts of Roman Christianity. They were the braintrust of European civilization, even if they were not demographically self-sustaining.

To a great extent the last ten years has seen a refutation of “pots not peoples.” It turns out that many of the archaeological transitions seen in the physical record correlate with demographic changes inferred from genetic changes. And yet we know from history that some peoples and social groups which were highly influential left far less of a demographic footprint. I suspect that the rise of cities and complex polities transformed the “pots not peoples” calculus significantly.

* Google the fact that about ten years ago Stark was dismissing reports that Americans were getting more secular as wishful thinking by biased liberal scholars. Who do you really think had a bias with hindsight?

Selection is going on with SLC24A5….

Filed under: Human Population Genetics — Razib Khan @ 12:20 am
The ancestral allele for rs1426654 at SLC24A5

 
On this week’s episode of The Insight, I talked to Matt Hahn about why he wrote his new book, his opinions on “Neutral Theory”, and what he thought about David Reich’s op-ed. Without Spencer’s supervision, I have to admit that I think I lost control and just went “full nerd”. Next week we’re dropping Carl Zimmer’s podcast, so rest assured that the world will come back into balance, and The Insight will be more welcoming to civilians!

At a certain point, Matt and I were discussing allele frequency differences between populations and he came close to saying all such differences between human populations were of modest frequency in relation to pairwise comparisons (e.g., 40% vs. 49%). Obviously, this is not true, because there is always the huge difference in SLC24A5 at SNP rs1426654 (at Duffy and a few other loci). A substitution of a G for an A converts the codon from alanine to threonine.

You have heard of this locus because of a paper in 2005, SLC24A5, a putative cation exchanger, affects pigmentation in zebrafish and humans. This paper came out in December of 2005, a few years after Armand Leroi wrote in Mutants that geneticists still hadn’t come to grips with normal variation in pigmentation in humans. The above publication was the first step in solving this question in the years between 2005 to 2010, at least to a good first approximation.

In the sample in the paper they explain 25-40% of the variation in melanin index between Africans and Europeans with this single genetic change (for various technical reasons it’s probably not that big an effect, though it is still big, and probably the largest effect quantitative trait locus for pigmentation in the human genome).

It turns out that this mutation, the derived variant, is almost disjoint is frequency between Europeans and Africans. That is, about ~100% of Africans carry the ancestry G base at while ~0% of Europeans carry the G base (as opposed to the A base). Interestingly, East Asians carry the G base at ~100% frequency as well. If you genotype an anonymous individual and their genotype is AG or GG on at rs1426654 then it is highly likely that that individual is not a European.

To give an example of how this works, in 2013 I stumbled onto a paper which genotyped 101 Europeans from Cape Town in South Africa. That means there are 202 alleles (two per person) at rs1426654. Of these, 5 of the alleles were ancestral (G). From this, I immediately concluded that it was highly likely that the Afrikaaner people of South Africa have non-European ancestry. I came to this conclusion because of 5 copies of the ancestral allele, ~2.5%, is shockingly high for a European population, and it was long surmised that the Afrikaaner people had some non-European heritage (Khoisan, Bantu, South and Southeast Asian) ancestry. The major of the whites sampled in Cape Town could have been Afrikaaners (I’ve confirmed this with genome-wide data).

To get a sense of where my intuitions come from you need to look at allele counts within populations. Using 1000 Genomes, Yale’s Alfred, and Gnomad I assembled a representative list to give you a sense of what’s going on. Using 126,548 counted alleles in Gnomad for individuals of European (non-Finnish) descent you see that 0.38% out of the total, 486, are ancestral.

Population Ancestral alleles Total alleles Freq
Samaritan 0 74 0%
Basque 0 216 0%
Greeks (Thrace, Athens) 0 184 0%
Burusho 0 50 0%
Pandit Brahmin, Kashmir 0 40 0%
European (Non-Finnish) 486 126548 0%
Ashkenazi Jewish 47 10148 0%
European (Finnish) 329 25790 1%
Iraq Kurds 1 68 2%
Yemenite Jews 2 78 3%
Havyaka Brahmin, Karnataka 2 62 3%
Palestinian 4 122 3%
Gujarati 10 206 5%
Tunisian Berber 6 110 5%
Andalusian 14 252 6%
Iranian 6 84 7%
Pashtun 21 190 11%
Uttar Pradesh Brahmin 4 34 12%
Pandit Brahmin, Haryana 13 78 17%
Punjabi 42 192 22%
South Asian 6921 30774 22%
Kalash 14 48 29%
Telugu 71 204 35%
Bangladeshi 80 172 47%
Sri Lanka Tamil 105 204 51%
Adi-Dravida, Karnataka 21 34 62%
Masai Kenya 192 286 67%
Austro-Asiatic tribe, Odisha 43 56 77%
Luhya Kenya 155 188 82%
Hausa 68 76 90%
Mende Sierra Leone 155 170 91%
Gambian 209 226 92%
Ibo 90 94 96%
Austro-Asiatic tribe, Odisha 92 96 96%
Esan Nigeria 193 198 97%
Yoruba Nigeria 213 216 99%
Biaka 135 136 99%
East Asian 18728 18856 99%
Ghana 140 140 100%
Mbuti 74 74 100%

Last fall Crawford et al. reported that rs1426654 is embedded in a haplotype that’s about ~30,000 years ago. Additionally, they contend that its presence within Africa is probably no earlier than the Holocene, the last ~12,000 years.  Martin et al. report that KhoeSan exhibit higher frequencies of the derived allele because of Eurasian back-migration and then in situ natural selection. Of course, not all Eurasians. Most East Asians have the ancestral variant of rs1426654.

This leaves us with West Eurasians, North Africans, and South Asians. I’ve put a few South Asian populations in the list to show you that there is a wide range of variation in allele frequencies. The South Asians in Gnomad, probably mostly Diaspora, have the ancestral variant at only 22%. In contrast, Austro-Asiatic speaking South Asian groups from northeast India have very high frequencies of the ancestral variant. There has clearly been in situ selection in some South Asian populations for the derived variant at rs1426654. Ancestral North Indian groups (ANI) probably brought the derived allele, and Ancient Ancestral South Indians (AASI) probably tended to carry the ancestral allele, like East Eurasians and Oceanians. Additionally, South Asian populations often have high drift. Some of the differences in the Alfred data seem to be impacted by this.

The situation in the Middle East, North Africa, and Europe is different.  In the Middle East and North Africa, the ancestral variant is present at frequencies around 1-10%.  Some of this can probably be attributed to admixture from Africa and in some cases South and East Asian populations. Ancient DNA from the Middle East and North Africa presents a mixed picture. The farmers who brought the Neolithic to Europe carried the derived variant at rs1426654, and some of the ancient Middle Eastern samples carry it. But not all. The recent Iberiomauserian samples which date to ~15,000 years ago don’t seem to have had the derived variant.

Though the hunter-gatherers of Western Europe only seem to have carried the ancestral variant at rs1426654, the hunter-gatherers of Scandinavia and Eastern Europe did exhibit the derived variant in some frequency, though lower than modern Europeans.

My own hunch is that the original genetic background against which the A mutation at rs1426654 emerged will be found increasing in frequency first somewhere in the Near East after the Last Glacial Maximum. But no ancient population shows the frequencies of the derived variant we see in modern Europeans. In isolated populations subject to drift it wouldn’t be surprising if the ancestral variant decreased to ~0%, But in European populations today in the vast majority of cases the ancestral variant is far lower than 1%, even though we know that within the last 10,000 years the ancestral populations streams had several groups with very high frequencies of that ancestral variant. The low frequency is not due to a freakish bottleneck all across Europe. It has to be selection

One thing I have pointed out is that this very low frequency of the ancestral variant indicates that the advantage at rs1426654 for the A allele in Europe is additive. In Northern Europe, the frequency of the derived variant that confers lactase persistence tops out at around ~90 percent. We know this region of the genome has been targeted by natural selection, but lactase persistence also happens to express dominantly genetically. That is, one variant of the mutant allele confers the phenotype. Once you hit ~90 percent of the derived variant only ~1 percent of the population would be lactose intolerant homozygotes (two copies of the ancestral variant). In the Gnomad sample of 60,000+ Europeans, they count three homozygote genotypes rs1426654. That’s 0.005%.

Something is happening at rs1426654. Selection. But why? No one really has any explanation beyond the obvious.

May 22, 2018

Our Edo period future?

Filed under: Edo period,History — Razib Khan @ 11:52 pm

The second season of Westworld has some scenes set in Edo period Japan. To spoil things for you there is apparently a scene-by-scene re-creation of a plot arc from the first season of the show set in the American West. Watching this scene, and comparing it to the earlier version, I can’t but help feel that the Edo period setting is more grand and refined. If the first season’s violent attack was brutalist, the scene above is more neoclassical.

Then again, Edo Japan and the American West are perhaps antipodes of second-millennium civilization. Where the 19th century American West was anarchic, chaotic, and creative, the Edo period in Japan was notable for its stability, order, and the perception that it was a culture in chrysalis. Old forms may have been reinvented, but those forms were treasured.

The context for the Edo period is that 16th century Japan was a dynamo. Not always in a good way. The islands were riven by internal warfare. The Japanese were known to be a piratical race by the Ming dynasty, and the 16th century ended with the warlord Hideyoshi’s disastrous invasion of Korea. Prefiguring Japanese ability to imitate the West in industriousness they developed a skill in the making of guns, while Roman Catholic Christianity had great success in the southern island of Kyushu.

Eventually, Tokugawa Ieyasu set the stage for Japan’s nearly three hundred year exile from the congress of nations, turning his back on Hideyoshi’s adventurousness. Of course, it is false to assume that the Japanese were totally insulated from the outside world. Not only did they connect with the West through the Dutch, but the Japanese maintained a more intense relationship with Korea. Even in the 17th and 18th century, a movement of “Western Learning” persisted through the interaction with the Dutch (though arguably late Confucian influences may have been more significant).

The violent suppression of Christianity in the 17th century and the emergence of a static caste system strikes modern sensibilities as brutal, barbaric and regressive. But the Edo period’s reduction in distribution and production of lethal firearms shows the upside of a conservative and controlling social land political elite. Violence continued, but it was relatively controlled and channeled.

We think of the future as endlessly protean and dynamic. But science fiction offers up an alternative possibility far more like Edo period Japan: technologically stagnant, culturally conservative. Frank Herbert’s Dune was set in the context of a universe where there had been a religious jihad against artificial intelligence. Meanwhile, Isaac Asimov’s Foundation series was originally based on imperial Rome, but later incarnations admitted that the better model was imperial China. Just as in the Dune series, the Foundation universe had to grapple with humanity’s protean and chaotic violence, which threatened to take down our civilization periodically due to enthusiasms.

The Edo period stretches from the early 17th century down to the middle of the 19th. All in all this is not a bad run. Our own republic’s 250 year anniversary will be on us in 2026.

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.

The tribe more diverse than all of Asia!

Filed under: Africa,Genetics,science — Razib Khan @ 1:17 pm
Bushman

In 2010, a paper, which sequenced the whole genome of Bishop Desmond Tutu, revealed that the San Bushmen of South Africa show more genetic difference between two men from different tribes than the differences between a European and an East Asian. In other words, two San Bushmen men from different populations within South Africa are more genetically distinct than a Chinese person is from a British person.

A follow-up paper from 2014 revealed that over the course of human history, the San Bushmen in fact had the “largest population” of any modern group. This seems surprising and ridiculous. There are over 1 billion Han Chinese, and only 100,000 San Bushmen.

Citation: Khoisan hunter-gatherers have been the largest population throughout most of modern-human demographic history

How can this be?

The first thing to keep in mind is that we’re talking about genetic diversity. When you look at the genome of a San Bushmen individual, it’s a lot more genetically diverse than that of a Han Chinese individual. A typical San Bushmen has more than 4 million genetic variants (SNPs), while a typical Chinese has only over 3 million genetic variants. This difference reflects population history.

One of the major keys to solving this mystery is to remember that the “Out of Africa” migration imposed a bottleneck on all non-African populations. That means that 50 to 100 thousand years ago, a small group of humans were the ancestors of all groups outside of Africa. All non-African populations exist in the shadow of this bottleneck, from the over 1 billion Han Chinese to a few hundred tribesman in the Amazon.

In contrast, the ancestors of Africans did not experience such a bottleneck.

The number of genetic variants that Africans carry did not decrease due to an “Out of Africa” bottleneck, and of all the people of Africa, the San Bushmen seem to have occupied a wide zone of southern Africa in their current state from an immemorial time. This stability has left an imprint on their genome, which is more genetically diverse than any other human group.

If you could use a time machine to count the number of people in the groups of humans which gave rise to the San Bushmen, they would always be larger than the small migration “Out of Africa.” This is why a tribe of San Bushmen have more genetic diversity than billions of Asians!

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


The tribe more diverse than all of Asia! was originally published in Insitome on Medium, where people are continuing the conversation by highlighting and responding to this story.

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