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In my free moments I have been reading R. Scott Bakker’s The Great Ordeal, as I needed to take a break from Congo: The Epic History of a People (I stopped before the Great War). As you might guess the latter is not a ‘feel-good’ work. And to be frank, The Great Ordeal is probably not the best choice to lighten the mood as a change of pace. It is one of the darkest and philosophically textured examples of the fantasy genre I’ve ever encountered, but that’s not surprising given Bakker’s previous works, and his background as an academic philosopher. Though the series does not indulge in as much graphic and visually rich descriptions of death and gore as George R. R. Martin’s A Song of Ice and Fire, it’s more deeply haunting and horrible. If Martin deals in shades of gray, from the honorable lightness of Jon Snow to the black depravity of Ramsay Bolton, Bakker’s characters seem to be swallowed by a blankness of color. Amorality rather than immorality.

Martin is a master of creating vivid characters with deep color who operate in a world of frenetic and engaging activity (at least up until the third book, when the plot was relatively fast). In contrast, Bakker’s plotting and characterization are both inferior, but that is in part because he gives more space over to a broader philosophical and moral framework, which hangs heavily over the whole narrative. Golgotterath and the Inchoroi are more memorable to me, alive in my imagination, than assorted protagonists swept up along the tides of history over the course of Bakker’s five books so far.

Where R. Scott Bakker excels, and where he rivals Tolkien in my opinion, is world building on a cosmic scale, complete with a well thought out mythos for humanity in his Secondary World. Bakker’s vision exhibits a great deal of verisimilitude, traversing humanity’s Bronze Age to the medieval period in ~4,000 years. The main actors within the narrative action are people from three of the races of men, of whom there are five total, and whose history goes back to an event termed the Breaking of the Gates, as humanity streamed into the western portion of the continent on which they reside, and engaged in a campaign of genocide against the Nonmen and their human servile caste, the Emwama.

Why am I regaling you with the narrative of a fantasy book series? Because the recent results out of ancient DNA and historical genetic inference of human prehistory suggest that the ‘make-believe’ narratives of epic fantasy may actually be an appropriate model of the formation of human populations in the wake of the Holocene. A friend of mine half-seriously quipped that the last 200,000 years of human history are a matter of collapsing ancient population structure. In fantasy novels often main characters themselves are exemplars of such broken population structure; the ‘half-blood’ trope as it were.

As a primal and backward looking genre fantasy dispenses with the need for a liberal individualist ethical framework, as historical relativism allows us to “put ourselves in the place” of protagonists whose motives and concerns are profoundly alien to moderns, albeit often with a sympathetic and contemporary twist. Jon Snow’s life to a great extent is motivated by his need to prove himself despite his bastardy. The specific motivation here would be hard to understand today, as legitimacy is not legally or normatively privileged as it has been historically, but the general need to find a place for yourself is one we can empathize with. Snow’s situation within a world of great noble houses and warring polities divided by region and language is one which most moderns are not comfortable with, but he is no revolutionary who yearns to overthrow the old regime. On the contrary, he is likely to play a large role in its maintenance and perpetuation.

Sargon_of_Akkad The meteoric rise of individuals from a humble station in the context of a static and hierarchical world are not aberrations on a world-historical scale. Sargon of Akkad, the first recorded emperor, whose dominion spanned multiple polities, was from a humble background. Gilgamesh, the scion of a noble family may be semi-mythical, but Sargon was a real person. On the edge of history, but a real person. In a world of corporate entities, defined by group identity, affinity, and affiliation, his success occurred though co-option of a system of city-states with roots over 1,000 years old at that point.

Sargon’s world is one whose outlines we are only vaguely aware of. There are many lacunae, not least of which the origins of the Sumerian people, who served to Sargon’s Akkadians the role of cultural progenitors. A linguistic isolate, the origin of the Sumerians is an unresolved mystery to this day. The end of the Sumerian cultural hegemony occurred in part due to the depredations of the Gutians, people from the hills of what is today Kurdistan, and rivalry with the people of Elam, from modern day Khuzistan.
Elam-mapThe linguistic affinities of the Gutians are unknown, while the Elamites, like the Sumerians, seem to be part of a linguistic isolate.

Much of this ignorance has to do with the importance of literacy in history. What we know about Elam is often through a Mesopotamian lens. The people of Sumer and Akkad, and later Babylonia and Assyria, saw Elam as the great enemy, the Persia to their Rome. The Gutians were a coalition of tribes from the mountainous areas to the east of Mesopotamia, and so had no real indigenous literate tradition. They do not even seem to have a distinctive enough archaeological tradition to trace their migrations.

F4.large Without text and material where does that leave us? Obviously we have a new method: ancient DNA. With this method one can infer demographic change by looking at patterns of genetic variation. The genetic relationship of various peoples who are “mysterious” to us today with modern populations will give us great insight. I predict that when the first results come back from Elamite Iran there will be a strong affinity to peoples in southern Pakistan, especially the Baloch and Brahui, as well as connections to India more broadly, above and beyond the expected local continuity.

Last week Science published a new paper on ancient Iranian genomes, from a period thousands of years before what I discussed above, Early Neolithic genomes from the eastern Fertile Crescent. It’s open access, so you can read it yourself, and I encourage you to do.

What makes this paper different from what has come before? Two things. The first is minor: better sampling. In particular, they have better regional sampling. For example, Iranian Zoroastrians (the link has plink format files). Second, and more important, they have at least one sample at 10x or more coverage. This means they can use haplotype based methods and make better calls on genotypes. It’s much more extensive in the supplements, but the authors discuss the functional characteristics of these populations more than in the earlier papers because of access to higher quality whole genome data. You need to be more confident at a specific locus when inferring function from that locus, than you need to be across the whole genome.

The phylogenetic portion reinforces what the earlier work argues: there were two great tribes of founding farmers who brought agriculture to North Africa, and Western & Southern Eurasia. Though the “cradles of civilization” were often in riverine landscapes, the agricultural revolution began in the Near East in the uplands, which would later become backwaters. Only here could primitive dryland agriculture take root in the desiccated landscape. This was the “Breaking of the Gates”.

There were, it seems, two major phases. The first phase was expansionary. The western farmers pushed outward to Europe and North Africa. The eastern farmers pushed toward South Asia and Central Asia. But look at the position of Iranians in the PCA, and the affinities within Iran. Modern Iranians are much more west shifted than you might expect from perfect continuity. Additionally, the haplotype affinities of populations to western vs. eastern farmers shows that Iranians today have much more affinity to western farmers than Iranian speaking people from Pakistan, especially the Baloch and Makrani in the southwest of the country. This is because there was a second phase: the great scrambling, when reflux from the west into Iran, and vice versa, erased the great division.

In the initial expansionary phased a stylized model was probably as good as any model. The world was dominated by hunter-gatherers, whose social-political ability to scale and organize was minimal. The farming populations probably began to organize chiefdoms rather early, and the spread of their lifestyle was to some extent at the tip of the spear. The hunter-gatherers fled, or were rapidly assimilated as subordinates, losing their cultural distinctiveness. But the next stage after the chiefdoms were more complex arrangements, which might transcend tribal loyalties, especially when one’s tribe spanned a continent.

A close look at the map shows that the Baloch and Sardinians have more affinity with these two ancient peoples than many of the groups which today occupy the Middle East. Why? Mostly because they are distinctive in being less subject to the reflux migrations in the wake of the Neolithic. And, if you look at Europe and South Asia, you can see that Indo-Europeans also left a stamp on these areas, by mediating gene flow from these tribes into areas where the other tradition had been dominant. Northern Europe is less biased toward western farmers than Southern Europe. Within South Asia, the most skewed bias toward eastern farmers are the Baloch, who happen to co-inhabit territory with a non-Indo-European speaking population, the Brahui. These Dravidian speakers are basically indistinguishable from the Baloch. Among the other groups, the Vishwabrahmin are biased toward eastern farmers. In contrast, the Tiwari, North Indian Brahmins, are more balanced. I believe this is because the Indo-Aryans brought western farmer ancestry with them from the steppe.

Rather than talking about the phylogenetic aspects anymore, I want to move to the functional considerations. It seems that the ancient eastern farmers did not have many of the adaptations that we associate with farmers. This is entirely logical. Much of our genetic character is the product of cultural changes, rather than cultural changes being the product of our genetic character. The null hypothesis should be that hunter-gatherers who had just taken to farming are basically like hunter-gatherers who adapted a new lifestyle.

But there are some intriguing elements of the pigmentation genetics, a topic I know a fair amount about. The results from this paper show that the derived variant of SLC24A5, the largest effect pigmentation allele we know of, was segregating in these farmers. This is not surprising. It was segregating in western farmers at high frequency as well. Among Caucasian hunter-gatherers, and even among hunter-gatherers from Mesolithic Sweden. It was, though, not so much found among Western European hunter-gatherers. It is totally fixed in Europe today in the derived variant. Curiously, the authors mention that SLC45A2, another skin-lightening derived allele, which is much more concentrated in Europe, has been found segregating in Neolithic Aegeans. So it may be that the two major skin-lightening alleles were introduced by western and eastern farmers. Finally, the allele known to produce blue eyes in Europeans, found in high frequencies in Mesolithic European hunter-gatherers, was also found segregating in WC1. WC1 is the highest quality genome in their ancient data, so this seems a likely inference.

What this tells us I think is that skin-lightening alleles have been segregating at appreciable frequencies for long time. They have a deep history. Periodically, a particular haplotype gets targeted for selection, and a sweep occurs. Personally, I am more and more leaning to the hypothesis that a diversity of functions and characteristics are the targets of this selection, with the phenotype often being a side effect. What is even more intriguing to me is that the peoples as distinct as Sardinians and Baloch don’t actually look that different physically. The great reflux even affected them, and with it perhaps came alleles which were selected upon and produced a relatively uniform phenotype from the Atlantic to the Indus?

Much of the prior understanding of history and prehistory has been driven by a banal and workaday conception of progress and change. Proponents of demic diffusion imagined stateless villagers pushing outward. Diffusionists assumed that techniques and material would flow along trade routes. There were no great disruptions, rather, there were evolutions and continuities.

That is not what ancient DNA tells us. In another context I’ve mentioned that ISIS is appealing to some because of its “heroic” narrative. Similarly, the origins of modern humanity may be much more heroic than we’d have thought. We the descendants of humans who crossed in Australia. The descendants of humans who finally made it to the New World. Would it be any surprise that nearer prehistory was as ground-breaking and tumultuous?

 
• Category: History • Tags: Prehistory 
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Dr. Joseph Pickrell has updated his preprint, The genetic prehistory of southern Africa, with some more material on the Sandawe. I’ve explored the genetics of the Sandawe a bit using ADMIXTURE, so I jumped straight to the section on ROLLOFF:

…To further examine this, we turned to ROLLOFF. We used Dinka and French as representatives of the mixing populations (since date estimates are robust to improperly specified reference populations). The results are shown in Supplementary Figure S22. Both populations show a detectable curve, though the signal is much stronger in the Sandawe than in the Hadza. The implied dates are 89 generations (2500 years) ago for the Hadza and 66 generations (2000 years) ago for the Sandawe. These are qualitatively similar signals to those seen by Pagani et al.[65] in Ethiopian populations. There are two possible historical scenarios that could lead to these signals: either the Hadza and Sandawe both directly admixed with a western Eurasian population about 2,000 years ago, or they admixed with an east African population that was itself admixed with a western Eurasian population. The latter possibility would be consistent with known east African admixture into the Sandawe[16] .

 

Pagani et al. refers to the paper Ethiopian Genetic Diversity Reveals Linguistic Stratification and Complex Influences on the Ethiopian Gene Pool, which inferred that the origin of the West Eurasian-African hybrid population of the Horn of Africa date to ~3,000 years B.P. Let’s back up here for a moment. First, it looks like the population of the Indian subcontinent came into being in its current state in the Holocene. Second, it also seems likely that there has been major disruption to the genetic substratum of Europe since the end of the last Ice Age. The top-line result is that a substantial minority of European ancestry, with a southwest-northeast cline, may be of East Eurasian provenance. But I think just as important is the possibility that there has been successive replacement of West Eurasian groups over the course of European prehistory. The genetic signal of the latter exists, but is more difficult to tease apart because these branches of the phylogenetic tree have a more recent common ancestor and are not as differentiated. Third, in historical time we have seen a massive reorganization in the center of Eurasia, as Iranian populations have given away to Turkic ones. Fourth, there is a fair amount of circumstantial evidence for massive population replacement across Southeast Asia of Negrito groups. First by the ancestors of Austro-Asiatics, and then Austronesians. Finally, now there are these confirmations of massive genetic turnover on the fringes of East Africa, from Ethiopia, down to the south in Tanzania.

One issue which now comes to mind for me is the nature of the people of Punt, a mysterious land, perhaps in modern day Somalia, which traded with antique Egypt. From the depictions in Egyptian wall art they do not seem to exhibit a conventional Sub-Saharan African appearance, despite their likely African location. And ancient Egyptians clearly were familiar with people of Sub-Saharan African appearance, as Nubians appear early on in their wall wart. But these results from ROLLOFF and Pagani et al.’s inference as to time of admixture give us a possible explanation: the people of Punt were outriders of Southwest Asian expansion into East Africa, and they exhibited an unadmixed appearance because admixture had not yet been extensive. Ultimate we’re taking para-history here. The people of Ethiopia were on the fringes of Egypt and the Near East, but at far enough of a remove that we are not treated to any literary documents which attest to the process of ethnogenesis.

This does not even touch upon the Bantu expansion, which seems to have occurred after the first intrusion of West Eurasians into the East African landscape. It is notable that the Sandawe as an amalgam of Khoisan and West Eurasian, while their Bantu neighbors presumably have less of both of these elements. When the pyramids were rising in Egypt all of this had not occurred.

(Republished from Discover/GNXP by permission of author or representative)
 
• Category: History, Science • Tags: Genetics, Genomics, Prehistory 
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pc1
Synthetic map

In the age of 500,000 SNP studies of genetic variation across dozens of populations obviously we’re a bit beyond lists of ABO blood frequencies. There’s no real way that a conventional human is going to be able to discern patterns of correlated allele frequency variations which point to between population genetic differences on this scale of marker density. So you rely on techniques which extract the general patterns out of the data, and present them to you in a human-comprehensible format. But, there’s an unfortunate tendency for humans to imbue the products of technique with a particular authority which they always should not have.

ResearchBlogging.org The History and Geography of Human Genes is arguably the most important historical genetics work of the past generation. It has surely influenced many within the field of genetics, and because of its voluminous elegant visual displays of genetic data it is also a primary source for those outside of genetics to make sense of phylogenetic relations between human populations. And yet one aspect of this great work which never caught on was the utilization of “synthetic maps” to visualize components of genetic variation between populations. This may have been fortuitous, a few years ago a paper was published, Interpreting principal components analyses of spatial population genetic variation, which suggested that the gradients you see on the map above may be artifacts:

Nearly 30 years ago, Cavalli-Sforza et al. pioneered the use of principal component analysis (PCA) in population genetics and used PCA to produce maps summarizing human genetic variation across continental regions. They interpreted gradient and wave patterns in these maps as signatures of specific migration events. These interpretations have been controversial, but influential, and the use of PCA has become widespread in analysis of population genetics data. However, the behavior of PCA for genetic data showing continuous spatial variation, such as might exist within human continental groups, has been less well characterized. Here, we find that gradients and waves observed in Cavalli-Sforza et al.’s maps resemble sinusoidal mathematical artifacts that arise generally when PCA is applied to spatial data, implying that the patterns do not necessarily reflect specific migration events. Our findings aid interpretation of PCA results and suggest how PCA can help correct for continuous population structure in association studies.

A paper earlier this year took the earlier work further and used a series of simulations to show how the nature of the gradients varied. In light of recent preoccupations the results are of interest. Principal Component Analysis under Population Genetic Models of Range Expansion and Admixture:

In a series of highly influential publications, Cavalli-Sforza and colleagues used principal component (PC) analysis to produce maps depicting how human genetic diversity varies across geographic space. Within Europe, the first axis of variation (PC1) was interpreted as evidence for the demic diffusion model of agriculture, in which farmers expanded from the Near East ∼10,000 years ago and replaced the resident hunter-gatherer populations with little or no interbreeding. These interpretations of the PC maps have been recently questioned as the original results can be reproduced under models of spatially covarying allele frequencies without any expansion. Here, we study PC maps for data simulated under models of range expansion and admixture. Our simulations include a spatially realistic model of Neolithic farmer expansion and assume various levels of interbreeding between farmer and resident hunter-gatherer populations. An important result is that under a broad range of conditions, the gradients in PC1 maps are oriented along a direction perpendicular to the axis of the expansion, rather than along the same axis as the expansion. We propose that this surprising pattern is an outcome of the “allele surfing” phenomenon, which creates sectors of high allele-frequency differentiation that align perpendicular to the direction of the expansion.

The first figure shows the general framework with which they performed the simulations:

pcab1

You have a lattice which consists of demes, population units, all across Europe. They modulated parameters such as population growth (r), carrying capacity (C), and migration (m). Additionally, they had various scenarios of expansion from the southwest or southeast, as well as two expansions one after another to mimic the re-population of Europe after the Ice Age by Paleolithic groups, and their later replacement by Neolithic groups. They modulated admixture and introgression of genes from the Paleolithic group to the Neolithics so that you had the full range where the final European were mostly Neolithic or mostly Paleolithic.

Below are some of the figures which show the results:

[nggallery id=25]

allesurAs you can see the strange thing is that in some models the synthetic map gradient is rotated 90 degrees from the axis of demographic expansion! In this telling the famous synthetic map showing Neolithic expansion might be showing expansion from Iberia. Perhaps a radiation from a post-Ice Age southern refuge?

One explanation might be “allele surfing” on the demographic “wave of advance.” Basically as a population expands very rapidly stochastic forces such as random genetic drift and bottlenecks could produce diversification along the edge of the population wave front. The reason for this is that these rapidly expanding populations explode out of serial bottlenecks and demographic expansions, which will produce genetic distinctiveness among the many differentiated demes bubbling along the edge of expansion. Alleles which may have been at low frequency in the ancestral population can “fix” in descendant populations on the edge of the demographic wave of advance. This is the explanation, more or less, that one group gave last year for the very high frequencies of R1b1b2 in Western Europe. With this, they overturned the classic assumption that R1b1b2 was a Paleolithic marker, and suggested it was a Neolithic one.

Here’s their conclusion from the paper:

A previous study showed that the original patterns observed in PCA might not reflect any expansion events (Novembre and Stephens 2008). Here, we find that under very general conditions, the pattern of molecular diversity produced by an expansion may be different than what was expected in the literature. In particular, we find conditions where an expansion of Neolithic farmers from the southeast produces a greatest axis of differentiation running from the southwest to the northeast. This surprising result is seemingly due to allele surfing leading to sectors that create differentiation perpendicular to the expansion axis. Although a lot of our results can be explained by the surfing phenomenon, some interesting questions remain open. For example, the phase transition observed for relatively small admixture rates between Paleolithic resident and Neolithic migrant populations occurs at a value that is dependent on our simulation settings, and further investigations would be needed to better characterize this critical value as a function of all the model parameters. Another unsolved question is to know why the patterns generally observed in PC2 maps for our simulation settings sometimes arise in PC1 maps instead. These unexplained examples remind us that PCA is summarizing patterns of variation in the sample due to multiple factors (ancestral expansions and admixture, ongoing limited migration, habitat boundary effects, and the spatial distribution of samples). In complex models such as our expansion models with admixture in Europe, it may be difficult to tease apart what processes give rise to any particular PCA pattern. Our study emphasizes that PC (and AM) should be viewed as tools for exploring the data but that the reverse process of interpreting PC and AM maps in terms of past routes of migration remains a complicated exercise. Additional analyses—with more explicit demographic models—are more than ever essential to discriminate between multiple explanations available for the patterns observed in PC and AM maps. We speculate that methods exploiting the signature of alleles that have undergone surfing may be a powerful approach to study range expansions.

What’s the big picture here? In the textbook Human Evolutionary Genetics it is asserted that synthetic maps never became very popular compared to PCA itself. I think this is correct. But, the original synthetic maps have become prominent for many outside of genetics. They figure in Peter Bellwood’s First Farmers, and are taken as a given by many pre-historians, such as Colin Renfrew. And yet a reliance on these sorts of tools must not be blind to the reality that the more layers of abstraction you put between your perception and comprehension of concrete reality, the more likely you are to be led astray by quirks and biases of method.

In this case I do think first-order intuition would tell us that synthetic maps which display PCs would be showing gradients as a function of demographic pulses. And yet the intuition may not be right, and with the overturning of old orthodoxies in the past generation of inferences from the variation patterns in modern populations, we should be very cautious.

Citation: Olivier François, Mathias Currat, Nicolas Ray, Eunjung Han, Laurent Excoffier, & John Novembre (2010). Principal Component Analysis under Population Genetic
Models of Range Expansion and Admixture Mol Biol Evol

(Republished from Discover/GNXP by permission of author or representative)
 
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Razib Khan
About Razib Khan

"I have degrees in biology and biochemistry, a passion for genetics, history, and philosophy, and shrimp is my favorite food. If you want to know more, see the links at http://www.razib.com"