Wednesday, March 28, 2012

Do Skulls Tell A Demic Diffusion Story?

Dienekes looks at statistical studies of skull shapes in different early European populations to argue, congruently with the limited available ancient DNA data, that Mesolithic hunter-gatherers in Europe were largely replaced by farmers who may in turn have been replaced to a meaningful extent by a subsequent farming population.

There are two (or three) puzzles in European prehistory:

How the robust, low-skulled, broad-faced hunter-gatherers became more high-skulled, narrow-faced and gracile?

How the latter became brachycephalized until early modern times?

Why they have become partially debrachycephalized in the most recent of times?

The answers to these questions turn to a great extent on the questions:

1. How much is facial structure genetic and how much is it a product of one's diet?

2. How rapidly can selective evolution take place in facial structure?

3. Is the two phased punctuated change in skeletal features quoted above an accurate characterization of the fairly rich body of ancient human remain evidence in Europe?

I'm probably less skeptical of Dienekes' propositions that there are punctuated changes in skeletal structure, and that these changes are due more to genes than to diet or rapid selective evolution within a population, than I was a few years ago.

In other words, the evidence I've seen over the past few years makes the hypothesis that a group of people with a distinctive physical appearance were to a great extent replaced (with a modicum of admixture blunting the trend) by a new group of people with a different distinctive physical appearance who had a technological and/or cultural advantage over the indigenes, on multiple occasions in prehistory, including one or two in Europe.

Plop an average 21st century American a la "The Magic Treehouse" books into a setting at the boundary between hunting-gathering lifestyles and farmings ones at the Neolithic transition in Europe (or for that matter, Bantu expansion in Africa), and he'd say that the newcomers and the existing population belonged to different races that were distinguishable on sight, at least, prior to significant admixture of the populations. Indeed, the differences in appearance were probably at least as stark as those between any two modern human populations in existence today.

Sure, there have been instances of dramatic cultural and/or linguistic change that are elite dominates and culturally diffused (Hungary's adoption of the Hungarian language, and Turkey's adoption of the Turkish language, and various mass religious conversions to Christianity, Buddhism and Islam are all examples).

There are also some examples of relatively equitable mergers to two different ethnic/racial groups, such as the merger of Austronesian mariners from Borneo and Bantu farmers from West Africa into the roughly evently admixed population of Madagascar (although linguistically, the Austronesians were dominant).

But, the transition from hunting and gathering to farming increasingly doesn't look like one of those historical moments in most of the places that we observe it.

The second, somewhat more subtle, transition that Dienekes' identifies is a plausible fit to a Bell Beaker/Indo-European transition era stone age to copper age transition in Europe. I've made the case in previous posts that this transition is the source of the Y-DNA R1b v. R1a divide in Europe, and that both haplogroups were probably rare before the transition, when Y-DNA haplogroups like G2a were more common. I've also pondered, although not with very solid evidence, if Y-DNA haplogroup I might be a strong candidate for a leading Paleolithic Y-DNA haplogroup.

The physical anthropology discipline of studying differences in skulls and other skeletal traits has something of a tainted reputation in the field, not the least of which because of its embrace of race-like concepts that American academics have memetic antibodies to considering seriously as science given the disasterous results that flowed from taking these ideas too seriously in the 18th and 19th centuries. But, that doesn't mean that the concept of migrations by and conflicts between "Peoples", rebranded as "demic diffusion," is an entirely useless construct as a first order approximation of the historical reality.

The abstract Dienekes cites on the latest study in this field is suitably cautious in framing its conclusions and transparent in revealing the assumptions upon which the conclusions are based.

Human Biology vol. 84

Cranial variation and the transition to agriculture in Europe

Ron Pinhasi, Noreen Von Cramon-Taubadel


Debates surrounding the nature of the Neolithic demographic transition in Europe have historically centred on two opposing models; a 'demic' diffusion model whereby incoming farmers from the Near East and Anatolia effectively replaced or completely assimilated indigenous Mesolithic foraging communities and an 'indigenist' model resting on the assumption that ideas relating to agriculture and animal domestication diffused from the Near East, but with little or no gene flow.

The extreme versions of these dichotomous models have been heavily contested primarily on the basis of archaeological and modern genetic data. However, in recent years there has been a growing acceptance of the likelihood that both processes were ongoing throughout the Neolithic transition and that a more complex, regional approach is required to fully understand the change from a foraging to a primarily agricultural mode of subsistence in Europe.

Craniometric data have been particularly useful for testing these more complex scenarios, as they can reliably be employed as a proxy for the genetic relationships amongst Mesolithic and Neolithic populations. In contrast, modern genetic data assume that modern European populations accurately reflect the genetic structure of Europe at the time of the Neolithic transition, while ancient DNA data are still not geographically or temporally detailed enough to test continent-wide processes. Here, with particular emphasis on the role of craniometric analyses, we review the current state of knowledge regarding the cultural and biological nature of the Neolithic transition in Europe.

The quote from the paper that Dienekes' analyzes and comments upon is also a pertinent one that clarifies the study's conclusion:

"Nonetheless, the craniometric analysis allows us to discern certain patterns. For example, the ‘Forest Neolithic’ specimens are clearly much more similar to other Mesolithic hunter-gatherers than to Neolithic farmers in terms of their craniometric shape, suggesting a large degree of cultural diffusion in this region. However, it is also evident that the earliest potential colonisers of southeast and central Europe are very similar to the Anatolian Çatal Höyük population, congruent with an initial demic diffusion from the Near East/Anatolia."

The "Forest Neolithic" included pottery-using groups of eastern Europe (hence Neolithic, since pottery is one of the hallmarks of that period), but should not be confused with the early agriculturalists who apparently practiced farming without pottery early on in the Near East and Greece, and then acquired pottery and expanded with it into the rest of Europe, together with their full "package" of domesticated crops and animals.

Thus, in the case of the forest people, there was cultural diffusion, while in more prime farming lands, immigrants largely replaced the native populations.

When Did African mtDNA reach Europe?

Two-thirds of African mtDNA haplogroups observed in Europe (which make up less than 1% of the total, but more in much of Southern Europe) are attributable to the last 3000 years or so.

Another one-third of African mtDNA haplogroups observed in Europe are considerably older, possibly arriving in Europe about 11,000 years ago, which was before herding and farming (the Neolithic revolution) arrived in Europe. Alternately, these mtDNA lineages may have merely been present in Southeastern European or West Asian sources of Neolithic migrants to Europe and arrived in Europe as part of those populations.

None of these mtDNA haplogroups are likely to have been present in Europe prior to the Epipaleolithic period.

Genome Research DOI: 10.1002/ajpa.22052

Reconstructing ancient mitochondrial DNA links between Africa and Europe

María Cerezo et al.


Mitochondrial DNA (mtDNA) lineages of macro-haplogroup L (excluding the derived L3 branches M and N) represent the majority of the typical sub-Saharan mtDNA variability. In Europe, these mtDNAs account for less than 1% of the total but, when analyzed at the level of control region, they show no signals of having evolved within the European continent, an observation that is compatible with a recent arrival from the African continent. To further evaluate this issue, we analyzed 69 mitochondrial genomes belonging to various L sublineages from a wide range of European populations. Phylogeographic analyses showed that ∼65% of the European L lineages most likely arrived in rather recent historical times, including the Romanization period, the Arab conquest of the Iberian Peninsula and Sicily, and during the period of the Atlantic slave trade. However, the remaining 35% of L mtDNAs form European-specific subclades, revealing that there was gene flow from sub-Saharan Africa toward Europe as early as 11,000 yr ago.


From here (with emphasis from me rather than the source). There are also Supplemental Materials.

The mtDNA mutation rate dating system used is more reliable as a measure of relative dates than it is of absolute dates. There are serious disputed regarding the calibration of these dates, although they do have a decent record of being correct at an order of magnitude level, at least. An estimated age of 3,000 years is probably not really 30,000 years, and visa versa. Dates based on mtDNA mutations seem to be more reliable than dates based on Y-DNA mutations, where fundamental irregularities have been demonstrated.

For example, the data strongly disfavor an interpretation that any of these lineages arrived in Europe or Asia during the Out of Africa migration from Africa of proto-Eurasians, even given all of the caveats that apply to mtDNA mutation rate based dates. The only mtDNA L3 haplogroup (all Eurasian mtDNA haplogroups derived from mtDNA subhaplogroup L3) for which an age of arrival in Europe could be estimated, L3d1b1a, was estimated to be 2,200 to 5,100 years old (most likely 3,600 years old), and is not particularly basal in the mtDNA L3 phylogeny.

The mtDNA data only trace matriline descent, and do not show all sources of a person's ancestry, although, all other things being equal, at a population level they are likely to be fairly representative of the mtDNA mix in a reasonable decent sized source population.

The study had a sample size of 69, with most coming from Southern Europe. The potentially European origin lineages were L1b1a8 and L1b1a12 (possibly Iberian rooted), and L2a1k (with one example in the Czech Republic and another from Slovakia).

According to Wikipedia discussing the geographical roots of the lineage that includes the possibly European Iberian lineages: "Haplogroup L1b is most frequent in West Africa specially in Senegal at 17-20%, and among Nigerian Igbo, Mauritanians, El Hierro, Gran Canarians, Akan people, Algerians, the Lemba, and Egyptians."

A prehistoric migration of women who could be the source of these mtDNA lineages to Spain across the Straits of Gibraltar (which has been the route of other prehistoric migrations documented with genetic evidence) is not too much of a stretch to imagine.

Similarly, per Wikipedia, discussing the geographical roots of the lineage that include the possibly Czechoslovakian lineage:

The wide distribution of L2a and diversity makes identifying a geographical origin difficult. The main puzzle is the almost ubiquitous Haplogroup L2a, which may have spread East and West along the Sahel Corridor in North Africa after the Last Glacial Maximum, or the origins of these expansions may lie earlier, at the beginnings of the Later Stone Age, ∼40,000 years ago.

In East Africa L2a was found 15% in Nile Valley- Nubia, 5% of Egyptians, 14% of Cushite speakers, 15% of Semitic Amhara people, 10% of Gurage, 6% of Tigray-Tigrinya people, 13% of Ethiopians and 5% of Yemenis.

Haplogroup L2a also appears in North Africa, with the highest frequency 20% Tuareg, Fulani (14%). Found also among some Algeria Arabs, it is found at 10% among Moroccan Arabs, some Moroccan Berbers and Tunisian Berbers. . .

[L2a1] is observed in West Africa among the Malinke, Wolof, and others; in North Africa among the Maure/Moor, Hausa, Fulbe, and others; in Central Africa among the Bamileke, Fali, and others; in South Africa among the Khoisan family including the Khwe and Bantu speakers; and in East Africa among the Kikuyu from Kenya. Closely related variants are observed among the Tuareg in North Africa and West Africa and among the East African Dinka and Somali People. . . . All Ethiopian L2 lineages can be seen as derived from the two subclades L2a1 and L2b.

How these lineages could end up in a quite differentiated form in Czechoslovakia in prehistoric times is any one's guess, although it is notable that many of the populations that share related lineages were historically nomadic.

It is also possible that L1b1a8, L1b1a12, and L2a1k are simply low frequency African lineages whose more recent African roots have not been discerned in Africa to due to sampling issues in Africa, or due to misfortunes that befell the source population in Africa during the historic era. In this scenario there may have been differentiation within the putatively European lineage within African populations, and a migration of multiple women who were members of this already differentiated African populations that has not been sampled in Africa to Europe could create the false appearance of European a rooting of these lineages. Given that every single African mtDNA subhaplogroup in Europe was analyzed that likelihood that something of this nature could have cropped up in the analysis due to African sampling related issues (where sampling strategies are often limited by practical and geopolitical considerations) is considerable.

The methods used in this paper are more useful in convincingly establishing that a migration of people with a particular mtDNA lineages to Europe was recent than it is in convincingly establishing that people with a particular mtDNA lineage arrived in Europe prior to the historic era.

Also pertinent is a recent paper summarizing the main points that argue for North African influences on the South Iberian Neolithic. To the extent that other lines of evidence support North African interaction with Southern Iberia about 8,000 years ago, attributing mtDNA lineages L1b1a8 and L1b1a12 in Europe to this event, which is within the mtDNA mutation date confidence interval in the mtDNA paper, makes a fair amount of sense.

Of course, this still does little to explain why there are two, fairly divergent permutations of mtDNA haplogroup L2a1k in modern Czechoslovakia that look like they've been in Europe since the Epipaleolithic.

On one hand, the fewer outliers there are, the more acceptable it is to propose that something really weird made them happen.

On the other hand, it is hard to see how a 14,000 year old mtDNA lineage would survive, but just barely, over that kind of time frame beginning so close to the founder population. You'd expect an mtDNA lineage that has survived so long to either have been wiped out, or to have grown to make up a larger percentage of the total sample and greater geographic range, in the course of fourteen thousand years. The hypothesis that a lineage like that which is still in the population, but appears only twice in the entire mtDNA catalog of Europe, has really been in Europe that long stinks a little from the point of view of statistical intuition.

Monday, March 26, 2012

Murray Gell-Mann Skewered In Comic

A link to a post analyzing the comic is here. It has the appeal of being a delightful "in joke" particularly pertinent to someone who blogs about both physics (where Murray Gell-Mann was undoubtedly a giant among men) and linguistics (where his high profile publications have been mediocre yet sensational and controversial).

I can't help but be uncomfortable at just how mean spirited the comic is in a case like this with an obvious, if unnamed, target, however deserving. At common law, and in older criminal statutes (e.g. Colorado Revised Statutes, Section 18-13-105 (2011)), there were two categories of criminal libel that did not involve reputation damaging falsehoods. One involved statements "tending to blacken the memory of one who is dead" and the other involved statements the "expose the natural defects of one who is alive," in either case, exposing the perosn to public hatred, contempt, or ridicule. I don't favor criminalizing either of these kinds of statements, but that doesn't mean that either kind of statement is in good taste in the company of decent people.

Still No Evidence Of SUSY At LHC

The latest round of LHC data further push up the mimimum masses of SUSY particles, if they exist at all.

If the squarks are outside of the LHC reach the lower limit on the gluino mass is now above 900 GeV, whereas if the squarks and gluino have comparable masses the limits on both are approaching the impressive value of 1.5 TeV.

The limitation on superpartner masses is model dependent, however:

[L]imits on the masses of the superpartners of the top quark still do not exist in a robust form. It is logically possible that the stop masses are relatively small, close to that of the top quark, while other colored superpartners are much heavier than TeV. This sort of spectrum is harder to achieve from the model-building perspective, but is favorable from the point of view of naturalness: light stops would cancel the dominant contribution to the Higgs mass from the induced in the Standard Model by the top quark. If that sort of spectrum is realized in nature then the limits discussed in the previous paragraphs do not apply, mostly due to the fact that the stop pair production cross section at the LHC is much smaller than that of gluinos and 1st generation squarks.

Of course, even if LHC doesn't find so much as a whiff of SUSY, one can still devise some sort of SUSY model with sufficiently heavy superpartners, or otherwise elusive phenomonology, to fit this data to some sort of model. Predictions made by SUSY theorists and string theorists, pre-LHC, aren't panning out. Even string theory backers are starting to sound disenheartened (I'm referring the the quoted material in the linked post, not the anti-SUSY blog author whose post is linked). So far, an experimental necessity for SUSY (or any beyond the Standard Model physics outside the neutrino sector) still isn't there and the entire theory is looking like one of the most expensive rabbit holes in the history of the human scientific endeavor.

Ancient Autosomal DNA Confirms Uniparental Conclusions

There are many samples of ancient mitochondrial DNA, fewer samples of ancient Y-DNA, and fewer still samples of ancient whole autosomal genomes. But, a new examination of four ancient autosomal DNA samples from Scandinavian individuals ca. 3000 BCE, three farmers and one a hunter-gatherer, confirms prior gentic evidence.

Analysis of these sequences in the context of the present day European gene pool suggests that the spread of agriculture involved the northward migrations of farmers. Thus, these data provide the most direct and compelling support for the demic diffusion model of agriculture (as opposed to cultural diffusion) described to date.

Razib, at Gene Expression, draws his conclusions more cautiously. He cautions against all or nothing conclusions, suggests that farmer colonization may have tracked fertile crop growing areas rather than broader geographic distances, and refers to violent conflict at martime boundaries. He concludes:

It seems likely that the expansion of agriculture was more spatially patchy, and exhibited more starts and stops, then the samples we have allow us to infer with any confidence. The arrival of startlingly distinctive populations genetically and culturally across which likely rapidly traversed territory in a point-to-point fashion, and their subsequent extinction or assimilation into local substrate, is less surprising when we keep in mind the discontinuous nature of much of cultural change.

Still, estimates that put the contribution of immigrating farmers to the gene pool at something on the order of 80% relative to European indigeneous hunter-gatherers, with a fair amount of regional variation, seems to be in the ball park of the indications from the evidence. The case, for example, for elite domination by immigrant farmers, who culturally transferred a farming package to a subordinate predominantly indigeneous population, at least in Europe, is weakening in the face of ancient DNA data.

Similarly, DNA studies of modern populations suggest that while modern Bantu language speaking populations in Africa sometimes assimilated a substantial share of indigeneous hunter-gatherer populations, that there was also almost alway a meaningful demic contribution of Bantu immigrants as well.

Monday, March 19, 2012

QCD With Monte Carlo Methods

For the last fifty years we have know pretty much exactly the laws of the universe that govern how atoms and their subcomponents quarks, are held together. But, the equations have been too hard to produce accurate answers in even moderately complex systems. Now, someone has come up with a mathematical trick that makes approximating the outcomes that these equations predict possible to do on a practical basis.

It turns out to be much harder to do exact calculations with the strong force that governs how quarks interact by exchanging color charged gluons (QCD) than it is to do exact calculations with the electromagnetic force in which charged particles exchange photons (QED). At first glance, the equations seem very similar. Both involve adding up an infinte series all possible ways that the particles in question would interact, each of which has a Feynmann diagram corresponding to it. When you do it right, this gives you a probability distribution of the next state the system could be in, and you interate. The equations for the probabilities for any given Feynmann diagram are pretty similar, although the QCD equations are a bit more complicated. In practice, you can't get an exact answer for anything but the most stylized situations, but you can do an arbitrarily large number of calculations and get a good approximation. Until a development announced recently at Science Daily, you did that by starting with the biggest terms and working your way down until you were statisfied with the degree of accuracy that you achieved.

In a nutshell, QCD equations are harder because you need to calculate far more terms to get the same level of precision, because the terms in the QCD series get smaller more slowly than the QED series, because there are positive and negative values of three orthogonal color charges instead of one unified color charge that comes in value of zero, +/-1/3 and +/-1 in the same charge dimension, and because gluons interact with each other, while photons don't.

But, a new method has made it possible to do practical calculations in QCD far more efficiently even in systems that aren't grossly oversimplified. In essence, the new method does a statistical sampling of all the possible ways a system could turn out with greater precision each, rather than looking at every single way the system could turn out up to a certain number of terms each that is used as a cutoff.

What they discovered is a trick -- called Diagrammatic Monte Carlo -- of sampling the Feynman series instead of calculating diagrams one by one. Especially powerful is the Bold Diagrammatic Monte Carlo (BDMC) scheme. This deals with a partially summed Feynman series (Dyson's development) in which the diagrams are constructed not from the bare Green's functions of non-interacting system (usually represented by thin lines), but from the genuine Green's functions of the strongly interacting system being looked for (usually represented by bold lines).

"We poll a series of integrals, and the result is fed back to the series to keep improving our knowledge of the Green's function," says Van Houcke, who developed the BDMC code over the past three years.

The BDMC protocol works a bit like sampling to predict the outcome of an election but with the difference that results of polling are being constantly fed back to the "electorate," Prokof'ev and Svistunov add. "We repeat this with several hundred processors over several days until the solution converges. That is, the Green's function doesn't change anymore. And once you know the Green's function, you know all the basic thermodynamic properties of the system. This has never been done before."

Several days with several hundred processors may seem like a lot. But, the old industry standard was to use similar resources to get less accurate answers in several years of non-stop calculations. And, if you made a subtle error in formulating the problem that caused you to tell the computer to calculate the wrong things, then you got the wrong answer and everybody who could understand what you did wrong would hate you. Fortunately, not many people could understood what you did wrong and most of them lived in constant fear that they would screw up so they would snub you in private, rather than on live TV before an audience of millions of people who can understand exactly what you did wrong like a March Madness basketball player. But, those days may now be behind us.

Also, keep in mind that all quarks and all gluons come in a very small number of varieties, many combinations of which are identical to each other due to symmetry. So, once you can solve a given chunk of a problem, you've solved it once and for all, and can fit that piece like a lego into a larger system (well, actually, quantum mechanics isn't quite as kind as a lego set, but the piece about there being interchangable, perfectly understood subcomponents is right). So, for example, once you figure out the behavior of a particular component of a quantum computer at a given temperature, you're good and you never have to do it again. And, if you can pretty accurately model a sophistiated system in the five years that it used to take to figure out a trivally simple one, you may actually get a result that is visibly worth the effort.

Sunday, March 18, 2012

Dienekes' Argues For West African Admixture With Eurasians








Timing and Causes Of The Little Ice Age Elucidated

Carbon dating of moss entombed in Baffin’s ice revealed two sudden advances of the snow line that killed off the vegetation: a sudden cold spell between 1275 to 1300, followed by intensifying cold between 1430 and 1455. . . . These chillier conditions began during an especially active time for volcanoes. “The second half of the 13th century had the most volcanism of any period of the past 1,500 years,” says Alan Robock, an atmospheric scientist at Rutgers University in New Brunswick, N.J. . . . Polar ice samples have revealed just such a series of eruptions, says Robock: an especially big explosion somewhere in the world in 1258, and three smaller ones in 1268, 1275 and 1284.

But, why did the cold triggered by the volcanos last? Enlarged ice caps might explain this:

“It’s been hard to understand how volcanism could lead to such long-lasting cooling,” says Stephen Vavrus, a climate scientist at the University of Wisconsin–Madison. Sea ice may have been the secret to keeping Earth frosty. In simulations of global climate run by Miller’s team, volcanic eruptions stimulated the growth of Arctic ice. Normally, this ice would melt back during summer months. But a series of four explosions, each within a decade of the last, could have expanded the ice enough to make it stable, says Miller.

From Science News relying upon G. Miller et al., "Abrupt onset of the Little Ice Age triggered by volcanism and sustained by sea-ice/ocean feedbacks." Geophysical Research Letters. Vol. 39, January 31, 2012, p. L02708. doi:10.1029/2011GL050168.

Comments to the article at the Science News website suggest solar variability could also have been involved, for example, stating:

Solar variability during this period began after the Medieval Maximum with the Wolf Minimum (which started around 1280) followed by the deeper 90 year long Spörer Minimum (which started around 1460) and the 70 year long Maunder Minimum in 1645 and the milder Dalton Minimum which ended about 1820.

Another comment suggests comet and asteroidal debris as a possible driver for the climate changes that took place.

Of course, simply knowing how quickly colder temperatures took hold is itself valuable because it puts boundaries on what would and would not have been possible for flora and fauna to do in order to adapt to the climate shifts.

The Little Ice Age, in turn, has been fingered as a major driving force behind some of the grand political trends of the Middle Ages.

Links between volcanic activity and major climate changes are also not new. One such spat of volcanic activity took place around the time that almost all of the Neanderthal population went extinct. An earlier spat of volcanic activity, associated with the Toba erruption, has been proposed as a driver of the expansion of modern humans into Eurasia.

Wednesday, March 14, 2012

Basque Y-DNA

Maju critically summarizes the results from the last paper on Basque Y-DNA, a companion to an earlier mtDNA piece by the same authors.

While I disagree with his premise that Y-DNA haplogroup "R1b1a2a1a1b (P312/S116), which is also the most important R1b sublineage worldwide, which I have called in the past the South Clade and will call hereafter as R1b-S, . . . [is] original from the Franco-Cantabrian Region and scattered with, possibly, Magdalenian culture." (i.e. 17,000 BP to 9,000 BP), apart from the issue over grossly overstating the time depth (my best estimate would be about a third of the age that he assigns to it), his analysis is solid and informative.

I also agree with him in doubting that Y-DNA haplogroup I is clearly Neolithic is its arrival in Europe; the evidence is less than clear one way or the other. Indeed, Y-DNA haplogroup I, which is probably quite a bit older than R1b, in my humble opinion, is one of the most plausible candidates for being a predominant Upper Paleolithic Y-DNA haplogroup for modern humans in Europe. Haplogroup I is most common in places that were either the last to succumb to farming, or where indigeneous populations would have had more staying power because they encounted migrant Neolithic farmers in its very formative stages when was not as dominant as would it become vis-a-vis people who didn't have more time to adapt to it in response to their own hunter-gatherer lifestyles. The overall frequency of Y-DNA haplogroup I in Europe (which varies quite a bit from region to region) is in the same ballpark as the frequency of mtDNA haplogroup U, the predominant Upper Paleolithic mtDNA haplogroup.

Afroasiatic Origins and the Afro-Dravidian Hypothesis

One collateral issue to the question of Afro-Asiatic origins discussed in two previous posts today (FWIW, those two posts and this one were mostly written about six months ago, but were awaiting final polishing and so didn't get posted until today), is the interrelationship between that question and the Afro-Dravidian hypothesis.

The Afro-Dravidian hypothesis argues that the Dravidian language is a derivative of an African language from the Niger-Congo family of languages, and that much of the cultural and technological packet associated with Dravidian culture has African origins. Frenchman Bernard Sargent is one of its principle advocates. I'm not entirely convinced of this hypotheis, but there is enough data to back it up to warrant giving the idea serious consideration, so I don't dismiss it out of hand either, as many do.

The linguistic evidence from within the Dravidian languages points to an origin of the Dravidian language of India around the time of the South Asian Neolithic ca. 2500 BCE. A few linguists have noted similarities between some Niger-Congo languages (particularly those on the Afro-Asiatic/Niger-Congo boundary area) and the proto-Dravidian language.

The crops used in early Dravidian agriculture were domesticated in and had their origins the African Sahel.

There are no meaningful African mtDNA traces in Dravidian South Asia that can't be attributed to events in the historic era, however, and the strongest outside Y-DNA signal, which coincides quite well with the locations of the proto-Dravidan society are rich in Y-DNA haplogroup T.

Given the fact that ancient peoples rich in Y-DNA haplogroup T were sailing the Red Sea and Indian Ocean from the Horn of Africa at the time, it makes sense that a male dominated group of people from the Horn of Africa might arrived on the east coast of India and bring new crops and technologies around 2500 BCE. Recent genetic profiles of tribal populations in India also support the inferrence that some of these populations may have genetic origins outside India in a time frame similar to that of the arrival of Indo-European and Austroasiatic food production and archeological cultures to India, rather than with the hunter-gatherers of India's deep indigeneous past. So, the fact that some of the high frequency Y-DNA haplogroup T populations in Indian are tribal populations doesn't necessarily contradict an Afro-Dravidian hypothesis.

The crops, technologies and potential linguistic links seem like a better fit to a Sahel agriculture, Niger-Congo language speaking people, however, than to a society that one might expect to be a Cushitic language speaking people then and there in what might have been the Kingdom of Punt or the Kingdom of Cush, which Y-DNA haplogroup T is currently common, and haplogroup T arguably looks like it has Egyptian or Mesopotamian origins, not Sahel African origins.

Why would people with overwhelming Egyptian/Mesopotamian patrilines speak a Niger-Congo language or be familiar with Sahel agriculture? Was Cushitic limited to areas further north at the time, and were Niger-Congo languages (driven by the expansion of Sahel agriculture) a layer present before Afro-Asiatic languages were in the Horn of Africa? Did ethnic Egyptians precede the Cushitic language in the sea trade of the Horn of Africa?

The "substrate" genetics of East Africa after one removes markers that look like Eurasian back migrations and also removes markers strongly associated with one or another Afro-Asiatic linguistic family, in uniparental and autosomal genetics, are distinctly East African and do not suggest prior genetic unity with West African populations prior to a very remote date (ca. 30,000+ years).

Another way to think about that fact is that East Africa has experienced at least two wave of Eurasian back migration. Sometime in the early Holocene (a period that bridges the Epipaleolithic and the Neolithic eras) associated with mtDNA haplogroups like M1 and U6. The other with the arrival of the Ethiosemitic languages. One plausible way to understand the spread of the Afro-Asiatic languages is to guess that it occured at the time of the early Holocene event. But, East Africa has a distinct genetic identity that predates either of these events and this identity is distinct from West Africa. West African sourced African genetics don't appear in East Africa until around the time of Bantu expansion into East Africa, contradicting the plausible thought that West Africans could have had notable demic influences on East Africa starting when the West Africans developed Sahel agriculture. (As Jared Diamond explains in "Guns, Germs and Steel", neither Sahel crops nor Fertile Crescent crops do well in the other's climate due to their differing seasonal patterns, although Sahel crops can do well in the monsoon climate of Southern India which has a seasonal pattern similar to the African Sahel.)

One possibility is that Horn of Africa people who could have brought the cultural package of Sahel agriculture to India may have themselves been recent recipients of that cultural package and experienced language shift in an early wave of Bantu, or pre-Bantu, expansion from West Africa, that was limited to a cultural/political elite and that the Niger-Congo language may have experienced similar linguistic trends to other languages on the Niger-Congo/Afro-Asiatic linguistic border like Swahili and some of the Niger-Congo languages spoken in the general vicinity of Senegal.

Afro-Asiatic Linguistic Origins From Historic and Linguistic Perspectives

The Afro-Asiatic languages are one of the major language families in existence today. Its main subfamilies are Semitic (e.g. Arabic, Hebrew, Aramaic (Levant), Ahmaric (Ethiopia), Maltese), Chadic (most Hausa, the language of a group of Sahel peoples who were traditionally pastoralists), Berber (particularly Tuareg, a group of North African pastoralists), Cushitic (generally in the vicinity of Ethiopia, Eritrea, and Somalia), Omotic (a small language family spoken in a small area on the Western fringe of the Cushitic area), and Coptic (once the language of ancient Egypt, now a liturgical language of Coptic Christians).

This language family includes some of the oldest languages attested in writing.

The ancient Semitic Akkadian language and related dialects just documented in the Assyrian Dictionary completed this year has a rich written record dating back to around 2500 BCE. The Phoenicians who produced the predecessor to the modern Roman alphabet had a Semitic language, as did the Punic peoples spoke Semitic languages.

Coptic is the second oldest attested written language with hieroglyphs using it dating back to before 3000 BCE. Coptic writing is know to have existed at least five hundred years earlier than the earliest Akkadian writing.

Reconstructions of proto-Afro-Asiatic languages suggest origins at least as late as the Neolithic and probably Cacholithic (i.e. copper age).

One of the oldest cities known to the archaeological record, Jerico, is in the heartland of the Semitic linguistic area.

We know that the Egyptian Neolithic started around 6000 BCE, a couple of thousand years after it began in the Fertile Crescent from which the Egyptian Neolithic derived. One of the notable Egyptian specific contributions was the domestication of the donkey. It is plausible to think that languages and food production technology spread together as part of an overall Neolithic culture expansion (with and/or without a demic component) from the Fertile Crescent. Much of the Levant was subject to Egyptian political dominance for centuries during the Bronze Age.

A story of Afro-Asiatic language family expansion linked to food production technology is somewhat complicated by the fact that agriculture was developed independently in the Sahel with a set of crops different from those of the Fertile Crescent. But, there is less than a perfect consensus regarding when this happened. Some sources seem to indicate that it arose roughly contemporaneously with Fertile Crescent agriculture, while some indicate that it happened much later. It is possible that Sahel agriculture was made possible, in part, by the arrival of domesticated animals from the Fertile Crescent Neolithic complex.

At any rate, it is not necessarily the case that Fertile Crescent agriculture was the sole source of food production technology in Africa. Ethiopia was also an innovator with a number of crop domestications of its own (e.g. coffee and certain local grains), but the timing of these domestications is fuzzy, although Ethiopian domestications were probably later than those in the Fertile Crescent and those of the Sahel.

Sahel crop domestication is tempting to associate with the development of the Niger-Congo languages.

Likewise, tropical food production can be associated pretty strongly with the later Bantu expansion (the largest subset of the Niger-Congo languages) and perhaps also with Austonesians who brought foods of Indonesian origin, like the bananna, with them across the Indian Ocean, and provided one of the main source populations of Madagascar.

All of this evidence suggests that linguistically, one theory that makes sense would be one in which the Afro-Asiatic languages have their roots either in Egypt or the Levant and spread with herding and/or farming from there. Egypt's dominion extended roughly to modern day Lebanon when it met its northern most match with the Hittites (the first historically attested linguistically Indo-European polity of any consequence in Anatolia).

Egypt's influence and trade connections also extended as far south as Ethiopia and Uganda. We have only a little information about the origins of non-Semitic, non-Coptic Afro-Asiatic languages. Archaeological cultures based on old pots and bones and tools have been described in the regions where these languages are spoken, although often not with the same level of detail as contemporaneous archaeological cultures of Europe, Asia and the Middle East. We have ancient Egyptian documents. The Egyptians described three kingdoms to the South of them: Cush, Punt and Yam, and described in detail the goods that they acquired from each.

There are Egyptian documents describing official delegations sent at least as far west as Lake Chad. Some historians of religion argue that the geography of the mythical Egyptian land of the dead corresponds to that of the Lake Chad region that this delegation describes, which is to towards the setting sun from the Nile basin, where Egyptian mythology would have expected the land of the dead to be located.

There is very little evidence, however, to suggest that Afro-Asiatic languages were ever spoken in Anatolia or that they were spoken in Mesopotamia prior to the arrival of Akkadian, although there are a handful of apparently Semitic root words in some of the oldest Sumerian documents, and some of the oldest cave wall art of the Caspian Sea region does depict boats that look very much like Egyptian ones in design.

There is likewise no evidence to support the possibility that Afro-Asiatic languages ever spread beyond the Mesopotamian plain. The Elamite language spoken in Persia in the time of Alexander's reign appeared to show no Afro-Asiatic influences.

I am not aware of any really good studies that pin down the strength and depth of the relationship between Coptic and Akkadian, the oldest written versions of two of the main Afro-Asiatic language families, for which there is the most suggestive evidence to support a case that one is the oldest Afro-Asiatic language family.

Even if the Afro-Asiatic languages originated in the Middle East (e.g. in Jerico, the oldest city known to mankind), it is entirely possible that all known Afro-Asiatic languages, including Semitic, are derivative of Coptic and that any earlier Fertile Crescent Afro-Asiatic languages died before they were noted in any historical records.


Tonal languages appear in the Omotic, Chadic, and Cushitic branches of Afroasiatic, according to Ehret (1996). As a prior post today noted, there is also an mtDNA L3 subhaplogroup connection between Chadic and Cushitic populations (that study probably didn't have an Omotic sample at all).

The Semitic, Berber, and Egyptian branches do not use tones phonemically.

How much weight to give to this tonality is hard to say. There is a fair amount of circumstantial evidence, when you look at patterns of semantic tone use globally in all sorts of languages, to suggest that tonality is more of an areal feature than it is an indicator of the ancestral source of a language. Neighboring languages that come from different families often share the feature of semantic tonality, while languages within the same language family often differ in their use of semantic tonality.

There have also been suggestions that tonality is part of a total phoneme set for a language and should be looked at as part of an evaluation of points like a languages consonant and vowel and click inventory. There are also been suggestions that the local climate and ecology can make certain phoneme sets better in some places than in others, that the nature of one part of a phoneme set influences the nature of other parts of the phoneme set, and that there are specific non-random factors that favor particular subtypes of phonemes in particular conditions.

Still, ultimately, a point of similarity between two languages is still a point of similarity and tends to indicate some connection between the two of some kind, and points of dissimilarity between two languages still tends to indicate a separation for some reason. Certainly, the fact that Chadic languages and Cushitic languages sometimes both have semantic tone, while Berber and Coptic and Semitic languages do not, does not hurt the argument that Chadic and Cushitic languages might have broken off from each other later than they broke off from other Afro-Asiatic languages.

North Semitic Languages

Akkadian and the related language Eblamite, appear to have their origins in the North Levant before becoming predominant in the formerly Sumerian language speaking Mesopotamian area which retained Sumerian as a liturgical language until about 100 CE, but made its first conversion to Akkadian around 2000 BCE (and later reverted temporarily to a non-Semitic language during a period of Kassite rule).

The Hebrew Bible doesn't really connect with historical accounts until the Iron Age. For example, the Philistines don't arrive in the Levant until around 1180 BCE (they were exiles from Mycenean Greece during Bronze Age collapse and were one of the "Sea Peoples"). The Biblical date for the arrival of the Jewish people in Egypt (using the Biblical estimate of 430 years from Jospeh to Exodus) roughly coincides with the rule of Egypt by Semitic Hyksos foreigners. Some of the oldest stories in the Bible, such as the Garden of Eden, Noah's flood, and the story of Moses, have well documented earlier strong parallels or geographic links to the Sumerian mythology of Mesopotamia. Hebrew is by most linguistic accounts one of the youngest branches of the Semitic language tree and Arabic is one of its closet linguistic relative, among language both living and dead.

Ethio-Semitic Languages

Linguists have pointed to all of the Ethio-Semitic languages within the Semitic language family arising from the introduction of a single proto-Ethio-Semitic language, probably from southern Arabia and have dated its rapid diversification in Ethiopia and Eritrea to around 800 BCE, although linguistic methods for dating the origin of languages is far from an exact science.

The oldest extant Ethiosemitic language is Ge'ez which survives primarily as a liturgical language of Ethiopian Orthodox Christians, Ethiopian Catholics and Beth Israel Jews. As noted in the link to Wikipedia above:

The Ge'ez language is classified as a South Semitic language. It evolved from an earlier proto-Ethio-Semitic ancestor used to write royal inscriptions of the kingdom of Dʿmt in Epigraphic South Arabian. Ge'ez language is no longer thought, as previously assumed, to be an offshoot of Sabaean or Old South Arabian, and there is linguistic evidence of Semitic languages being spoken in Eritrea and Ethiopia since at least 2000 BC.

However, the Ge'ez alphabet later replaced Epigraphic South Arabian in the Kingdom of Aksum (Epigraphic South Arabian letters were used for a few inscriptions into the 8th century, though not any South Arabian language since Dʿmt). Early inscriptions in Ge'ez and Ge'ez alphabet have been dated to as early as the 5th century BC, and in a sort of proto-Ge'ez written in ESA since the 8th century BC. Ge'ez literature properly begins with the Christianization of Ethiopia (and the civilization of Axum) in the 4th century, during the reign of Ezana of Axum.




The Kingdom of D'mt from around 700 BCE to 400 BCE in Eritrea and northern Ethiopia had a succession of about four kings (or possibly four dynasties), and was notable for its irrigated farming, plows, millet, and iron age technology. It collapsed into multiple successor states in different regions that were reunited into the Kingdom of Axum starting before 100 CE and lasting until around 960 CE.

One study links Ethio-semitic to Y-DNA haplogroupJ1c3 and there are distinguishable population genetic differences between Ethio-semitic linguistic populations and Cushitic and Omotic linguistic populations that indicate recent Eurasian admixture to a greater degree in Ethio-semitic populations.

The Baysean estimate of 860 BCE for a common Ethio-semitic, which roughly corresponds to proto-Ge'ez, is probably too young.

Cushitic and Omotic Languages

It is tempting to see the trade relationships of Egypt with these regions as the source of the Cushitic and Omotic languages (with Omotic possibly showing a mix of Nilo-Sharan languages such as Maasi, and Cushitic influence on the Cushitic fringe).

Records of trade expeditions to Punt seem to be a reasonable good fit for Somolia or Lake Albert, had a long running and strong trading relationship with Egypt (myhrr was one of its major exports), and trade with it is attested as far back as the 25th century BCE in Egyptian records (and probably dates back centuries earlier). So, Punt was a Kingdom that probably pre-dated the appearance of Ethio-Semitic languages in Africa and may have been a place where early Cushitic languages were spoken.

Yam appears to be a reasonably good fit for Northern Uganda and was a source for many animals and products associated with tropical Africa. Yam may also have been a major source of copper for Egypt, and in one instance was noted a the Kingdom from which a pygmy individual was brought to Memphis in Egypt.

Indeed, all of the presents attributed to the "Wise Men" in the Nativity story (gold, frankincense and myhrr) could reasonably have come from Punt and Yam, which are black African countries.

Cush was probably north of Punt and Yam and while being South of Nubia (in present day Sudan).

Berber languages

It is tempting to associate the Berber languages with the arrival of pastoralism from Egypt to the region. But, Berbers are genetically distinct from Arabs and Egyptians and show considerable genetic continuity with pre-Neolithic North African hunter-gatherers.

Chadic languages

Chadic languages may be appropriate to associate with the appearance of pastrolist, ceramic cultures that appeared in the region where they are now spoken around 4000 BCE.

There are a few references that seem to be to ancient Egyptian expeditions to Lake Chad, but there does not appear to have been regular, robust trade between Egypt and Chadic peoples in the same way that there as to Kingdoms like Punt and Yam. Some linguistics have hypothesized, however, that Chadic and Cushitic are part of the same branch of the Afro-Asiatic languages with a common linguistic origin in a single proto-language.


A 2010 paper by Cruciani, et al., has a nice summary of the Paleoclimatic factors in the Sahara against which the historical migrations and expansions would have played out (citations included):

Over the past thousands of years, the Sahara has undergone dramatic climatic oscillations including arid phases, during which it was largely uninhabitable, and humid episodes, which transformed the desert into a fertile landscape.1 After a hyper-arid period about 23–14.5kya, the Saharan region experienced a monsoonal moist climate, characterized by increased rainfall.2, 3 During the Holocene Climatic Optimum (about 10–5kya), a few thousand years after the beginning of the humid period, flora and fauna repopulated the desert, and a mosaic of savannah and woodland became well established throughout much of the Sahara.3 At the same time, the Sahara was home to giant lakes,4 the largest of which, the paleolake Megachad, may have possibly covered an area of at least 400000km2, more than the Caspian Sea, the biggest lake on earth today.5 This greening scenario was interrupted by a number of arid episodes, and at about 5–6kya, the region experienced a rapid onset of dryer conditions. These marked the beginning of a shift towards permanent aridity, with variations in the distribution and timing of these changes between the eastern and central/western Sahara.3 Human–environment interactions in the Sahara have been greatly influenced by these climate fluctuations.1

Close links between climatic variations and prehistoric human occupation of the Sahara during the early mid Holocene (10–5kya) are documented by archeological6, 7, 8 and paleoanthropological9, 10 evidence.

1.Brooks N, Chiapello I, Di Lernia S, et al. The climate-environment-society nexus in the Sahara from prehistoric times to the present day. J North Afr Stud. 2005;10:253–292.
2.Talbot MR. Late Pleistocene rainfall and dune building in the Sahel. Palaeoecol Afr. 1983;16:203–213.
3.Burroughs WJ. Climate Change in Prehistory. The End of the Reign of Chaos. Cambridge University Press: Cambridge; 2005.
4.Damnati B. Holocene lake records in the northern hemisphere of Africa. J Afr Earth Sci. 2000;31:253–262.
5.Drake N, Bristow C. Shorelines in the Sahara: geomorphological evidence for an enhanced monsoon from palaeolake Megachad. Holocene. 2006;16:901–911.
6.Breunig P, Neumann K, Van Neer W. New research on the Holocene settlement and environment of the Chad Basin in Nigeria. Afr Archaeol Rev. 1996;13:111–145.
7.Huysecom E, Ozainne S, Raeli F, Ballouche A, Rasse M, Stokes S. Ounjougou (Mali): a history of Holocene settlement at the southern edge of the Sahara. Antiquity. 2004;78:579–593.
8.Kuper R, Kröpelin S. Climate-controlled Holocene occupation in the Sahara: motor of Africa's evolution. Science. 2006;313:803–807.[PubMed]
9.Tafuri MA, Bentley RA, Manzi G, Di Lernia S. Mobility and kinship in the prehistoric Sahara: strontium isotope analysis of Holocene human skeletons from the Acacus Mts. (southwestern Libya) J Anthropol Archaeol. 2006;25:390–402.
10.Sereno PC, Garcea EAA, Jousse H, et al. Lakeside cemeteries in the Sahara: 5000 years of Holocene population and environmental change. PLoS One. 2008;3:e2995. [PMC free article][PubMed]

Were The Post-Holocene Arid Period Gobero People Chadic?

The abstract of the paper in footnote ten (also free access) provides (headings omitted) that:







The climate sequence described is suggestive of an association of the Chadic populations with the newcomers ca. ~5200-4600 B.C.E. who repopulated Gobero in Niger after the mid-Holocene arid period in the Sahara abated.

This time frame is particularly attractive because it is the most recent case of clear population replacement in the archaeological record in the Sahel, where the Chadic language speaking people are found, until the recent historic period. Similarly, early time frames are unattractive, because they are not in clear population continuity with modern populations, and because the population genetics of the Chadic people, mentioned in a separate post, are suggestive of a population that was intrusive to the region.

This date is also not too far out of line with the estimated split between Y-DNA haplogroups R1a and R1b, which is the timeframe that one would expect from a basal branching off from European R1b haplogroups.

In contrast, the Sahara's Holocene Climatic Optimum seems more plausible to associate with the emergence of the Niger-Congo language speaking people who would be displaced to the South in order to maintain their lifestyle as the Sahara aridified, and their Sahel agriculture. The current population of the Sahel shouldn't overlap too much with the pre-mid-Holocene arid period population there. The Niger-Congo linguistic community, unlike the Chadic linguistic community, also doesn't show clear signs of Eurasian genetic links.

The Gobero People's Contemporaries In Egypt

The Neolithic revolution appears in Egypt around 6000 B.C.E. and the Egyptian historic record goes back to about 3100 B.C.E., so these dates would be in a pre-historic period in Egypt, after it had adopted farming and herding, but before it had adopted writing.

Specific, the possibly proto-Chadic people at Gobero would be at the tail end of the Faiyum A culture in Egypt (ca. 6000 B.C.E. to 5000 B.C.E.). As Wikipedia explains regarding this culture:

Continued desiccation forced the early ancestors of the Egyptians to settle around the Nile more permanently and adopt a more sedentary lifestyle. The period from 9000 to 6000 BC has left very little in the way of archaeological evidence. Around 6000 BC, Neolithic settlements appear all over Egypt. Studies based on genetic, and archaeological data have attributed these settlements to migrants from the Fertile Crescent returning during the Egyptian and North African Neolithic. However, some morphological and post-cranial data has linked the earliest farming populations at Fayum, Merimde, and El-Badari, to local North African Nile populations.* The archaeological data suggests that Near Eastern domesticates were incorporated into a pre-existing foraging strategy and only slowly developed into a full-blown lifestyle, contrary to what would be expected from settler colonists from the Near East. Finally, the names for the Near Eastern domesticates imported into Egypt were not Sumerian or Proto-Semitic loan words, which further diminishes the likelihood of a mass immigrant colonization of lower Egypt during the transition to agriculture.



* The sources cited for this statement are: Smith, P. (2002) The palaeo-biological evidence for admixture between populations in the southern Levant and Egypt in the fourth to third millennia Bce. u: Egypt and the Levant: Interrelations from the 4th through the Early 3rd Millennium BCE, London-New York: Leicester University Press, 118-128; Keita, S.O.Y. (2005) "Early Nile Valley Farmers from El-Badari: Aboriginals or "European" Agro-Nostratic Immigrants? Craniometric Affinities Considered With Other Data". Journal of Black Studies, Vol. 36 No. 2, pp. 191-208; and Kemp, B. 2005 "Ancient Egypt Anatomy of a Civilisation. Routledge. p. 52-60.

Or, it could have coincided with the early part of the Merimde culture of Egypt (ca. 4800 B.C.E. to 4200 B.C.E.) which appears to have been derived from the Faiyum A culture. But, the funerary practices of the Merimde culture seem entirely unlike those described in the post-arid period people at Gobero. The Merimde people did not have cemetaries or have grave goods, both of which were distinctive aspects of the Gobero burials that were unearthed.

Gobero doesn't have metal artifacts, which would suggest that any Egyptian links may have predated the dawn of the copper age in Egypt ca. 4400 B.C.E. Timewise and based on geography, the Tasian culture of Upper Egypt, ca. 4500 B.C.E. coincides pretty closely with the emergence of post-arid period populations at Gobero.

The post-arid period people at Gobero would seem to predate the Badari culture of Egypt (4400 B.C.E. to 4000 B.C.E. and possibly as far back as 5000 B.C.E.) which is the first one in which direct evidence of agriculture is found. Given that the Badari culture showed strong signs of influences from the Western Desert, it isn't impossible that the Chadic people could have been an important source for the Badari culture, rather than visa versa.

The Gobero People's Contemporaries In The South Levant

The contemporaneous archaeological culture of the South Levant is called the Pottery Neolithic (see also here) and conventionally dated from about 5500 B.C.E. to 4500 B.C.E.

The Gobero People's Contemporaries In Europe

The contemporaneous archaeological cultures in Europe are the Linear Pottery Culture and late Cardium Pottery culture. Thus, this would envision the Chadic people as appearing in the African Sahel around the same time that the Fertile Crescent Neolithic spread to Europe, but in an expansion that was much less dominant in Africa than its European counterparts, presumably because the Fertile Crescent package was nearing its geographic extreme of usefulness there and because the Fertile Crescent package had competition from an indigeneous Sahel Neolithic associated with the Niger-Congo language family there.

The Chadic people may have had less local admixture, particularly patriline local admixture, than other Afro-Asiatic peoples, because the mid-Holocene arid period had left them with a largely vacant region of land to repopulate, while Neolithic migrants bearing the Fertile Crescent package elsewhere in the Afro-Asiatic region may have had to compete with proto-Neolithic populations that had sedentary fishing, hunting, pottery, jewelry, and perhaps even the gathering of pre-domesticated plant that were tended to some extent. Thus, an absence of early populations to dilute them could partially account for Chadic genetic distinctiveness.

However, the parallels between the Chadic arrival and the European early Neolithic shouldn't be overstated, because the Chadic mtDNA signature is closer to that of the Cushitic people than it is the early Neolithic populations of Europe.

Afro-Asiatic Languages and Uniparental Genetic Markers

There are several major groups of languages within the Afro-Asiatic languages: Semitic (e.g. Arabic and Hebrew), Chadic (e.g. Hasua), Berber (e.g. Tuareg), Omotic, Cushitic, and Coptic (i.e. ancient Egyptian). Discerning the pre-history of these languages is not easy. Neither language features, nor genetics offer a comprehensive pan-linguistic family answer. This post looks at Afro-Asiatic uniparental genetic markers (and was mostly written about six months ago, but never posted as it awaited some editing and polishing).

An analysis of autosomal Afroasiatic genetics appears in a recent post at Ethio Helix. In the Principle Component Analysis done for this dataset, "Component 1 separates Berber/Semitic/Egyptian speakers from Chadic speakers, with Ethiopian Semitic/Cushitic speakers plotting somewhere in between, but closer to the former in this separation. Component 2, separates Ethiopians+Egyptians from the rest. Component 3 Separates the Mozabites from the Rest, with Ethiopians again retaining an intermediate position." Looking at an Admixture analysis with K=5 in this data set on a chart the separates clusters in two dimensions whose distance from each other is based on FsT distance, "The biggest separation for both Axis is for the cluster I nicknamed Cushitic, while the Berber, Semitic and Mozabite clusters appear pretty close, with the Mozabites looking a bit isolated." Berber and Egyptian are close; Cushitic and Chadic are roughly as far from each other and the Egyptian-Berber-Mozabite cluster is from the Cushitic cluster.

Honestly, autosomal data, rather than clarifying the relationships, seems mostly just to muddy the waters further. The notion that Egyptians are more closely linked to Ethiopian populations than non-Ethiopian populations does emerge, however. Also, Egyptians do seem to be more genetically diverse than some of the other populations autosomally. They seem to have genetic components that don't overlap with other populations including the main "Egyptian" component, at a fairly high frequency.

Chadic Languages and Y-DNA R1b-V88

Chadic language speaking men have the most distictive genetic profile.

Although human Y chromosomes belonging to haplogroup R1b are quite rare in Africa, being found mainly in Asia and Europe, a group of chromosomes within the paragroup R-P25(*) are found concentrated in the central-western part of the African continent, where they can be detected at frequencies as high as 95%. Phylogenetic evidence and coalescence time estimates suggest that R-P25(*) chromosomes (or their phylogenetic ancestor) may have been carried to Africa by an Asia-to-Africa back migration in prehistoric times. Here, we describe six new mutations that define the relationships among the African R-P25(*) Y chromosomes and between these African chromosomes and earlier reported R-P25 Eurasian sub-lineages. The incorporation of these new mutations into a phylogeny of the R1b haplogroup led to the identification of a new clade (R1b1a or R-V88) encompassing all the African R-P25(*) and about half of the few European/west Asian R-P25(*) chromosomes. A worldwide phylogeographic analysis of the R1b haplogroup provided strong support to the Asia-to-Africa back-migration hypothesis. The analysis of the distribution of the R-V88 haplogroup in >1800 males from 69 African populations revealed a striking genetic contiguity between the Chadic-speaking peoples from the central Sahel and several other Afroasiatic-speaking groups from North Africa. The R-V88 coalescence time was estimated at 9.2-5.6 [corrected] kya, in the early mid Holocene. We suggest that R-V88 is a paternal genetic record of the proposed mid-Holocene migration of proto-Chadic Afroasiatic speakers through the Central Sahara into the Lake Chad Basin, and geomorphological evidence is consistent with this view.

From Cruciani, et al., "Human Y chromosome haplogroup R-V88: a paternal genetic record of early mid Holocene trans-Saharan connections and the spread of Chadic languages." Eur J Hum Genet. 2010 Jul;18(7):800-7. Epub 2010 Jan 6.

I am deeply skeptical of the data suggested (Dienekes' expedent of dividing estimates by three seems more on target and the entire business of dating Y-chromosomes by mutation rates is suspect), but the linguistic-genetic link is clear.

What is notable about this result?

As one of the five major Afro-Asiatic language families, the origins of this language family are important to understanding the origin of the Afro-Asiatic languages generally, a major unresolved issue.

The genetic case is strong that Chadic has its roots in Asia to Africa backmigration. The low levels of admixture between Chadic and non-Chadic speakers until very recently (the Fulani and Hasua are in the process of merging in ethnic identity to some extent right now), suggests that this relatively genetically distinct population is relatively new to the region relative to other languages.

Since language tends to track Y-DNA more than mtDNA, the strong Y-DNA traces suggest an origin for Chadic languages outside of Africa.

This branch of the Y-DNA R haplogroup is quite basal, so dating this split also puts a minimum date on expansion of the rest of the Y-DNA R haplogroup which is predominant in much of West Eurasia. The Y-DNA haplogroup R1b common among Chadic language speakers in the V88 subtype, however, is generally associated with Western Europe and tenatively, with Indo-Europeans, although the break of the African Y-DNA haplogroup V88 from other R1b haplogroups found in Europe would have happened a very long time ago.

Still, how any R1b haplogroup end up in a linguistically Afro-Asiatic population in the Sahel? This is a mystery.

R1b is not commonly found in Egyptians, Ethiopians, or Berbers.

Indo-Europeans are not attested historically anywhere in Mesopotamia, the Levant, or North Africa until the classical Greeks and Romans expand except at the fringes of the Hittite Empire of the Bronze Age.

Indeed, there is a plausible arguement that there weren't even any Indo-Europeans (and quite possibly very few men with Y-DNA R1b haplogroups) in Western European until the early Bronze Age, with Indo-Europeans possibly arising with the Bell Beaker culture. The Central European Neolithic, for example, up the Danube, is associated with Y-DNA haplogroup R1a (which is absent in Chadic populations), not R1b.

Anatolia is associated with Y-DNA haplogroup J2, which is absent in Chadic populations. South Semitic peoples are associated with Y-DNA haplogroup J1, which is absent in Chadic populations. One would think that migrations to Africa from either area would have included J2 or J1 in the Y-DNA mix of the population, although founder effects with a small founding population of related men could account for their absence as well.

R1b is not exclusively Indo-European, as it is found in the linguistically non-Indo-European Basque people (whose high levels of lactose tolerance suggest a pastrolist dairy utilizing economy for their ancestors), and in Central Asia (which was genetically and in phenotype basicallly European as far as the fringes of Mongolia in the early Bronze Age), but no one suggests that the Chadic and Basque languages have any connection whatsoever.

Anatolia and the Dead Sea are plausible sources based on the presence of basal Y-DNA haplogroup R1b types there. But, we don't really know how or when the genetic outlier pocket of population in the Dead Sea area, for example, ended up there. The population of the Dead Sea, for example, could be derived from refuguees from someplace else who finally found a place to settle in the Dead Sea area at some undocumented point of time in ancient times.

Overview of Y-DNA in Afro-Asiatic Linguistic Families

There are population genetic links to Eurasia in many of Afro-Asiatic populations. On the Y-DNA side, Y-DNA haplogroups T (common in Egypt, Ethiopia and Somolia), J1 (associated with Arabia and other Semitic populations including Ethio-Semitic populations), and R1b-V88 (associated with Chadic language populations) all probably have origins outside Africa. On the mtDNA side, haplogroups M1 and U6 are both probably Eurasian in origin. There are mtDNA similarities between Cushitic and Chadic populations, although their Y-DNA profiles are quite distinct. Also associated with Afro-Asiatic languages is Y-DNA haplogroup Eb3 associated strongly with Egypt and probably having an African origin.

As we look at Afro-Asiatic liguistic origins it looks like Chadic is an outlier genetically within the Afro-Asiatic linguistic family, but each of the Afro-Asiatic lingustic families has a pretty distinctive uniparental genetic marker profile. As Wikipedia notes (footnotes omitted):

The migration of Afroasiatic languages from their original homeland is often thought to have also involved the movements of significant numbers of people. Therefore, attempts have been made to associate Afroasiatic language groups with genetic markers.

The most commonly cited genetic marker in recent decades has been the Y chromosome, which is passed from father to son along paternal lines in un-mixed form, and therefore gives a relatively clear definition of one human line of descent from common ancestors.

Several branches of humanity's Y DNA family tree have been proposed as having an association with the spread of Afroasiatic languages.

Frequency of haplogroup E1b1b in select Afro-Asiatic speakers
Language (Region where historically spoken) Frequency
Cushitic 32–81%
Egyptian languages 36–60%
Berber languages 40–91%
Semitic languages 7–29%
Omotic languages 50%

1. Haplogroup E1b1b is thought to have originated in East Africa. In general, Afroasiatic speaking populations have relatively high frequencies of this haplogroup, with the notable exception of Chadic speaking populations. Christopher Ehret and Shomarka Keita have suggested that the geography of the E1b1b lineage coincides with the distribution of Afroasiatic languages.

2. Haplogroup J1c3 (Y-DNA), formally known as "J1e", is actually a more common paternal lineage than E1b1b in most Semitic speaking populations, but this is associated with Middle Eastern origins and has apparently been spread from there after the original dispersion of Afroasiatic.

3. Haplogroup R1b1a (R-V88), and specifically its sub-clade R-V69, has a very strong relationship with Chadic speaking populations. Unlike other Afroasiatic speakers, Chadic language speakers have low frequencies of Haplogroup E1b1b.

Frequency of Sub-Haplogroup R1b1a in select Afro-Asiatic speakers
Chadic languages -- 28.6-95.5%
Berber languages -- 0-26.9%
Semitic languages -- 0-40%
Egyptian languages -- About 14% of Sudanese Copts had R1b although they were not typed for the V88 marker which defines R1b1a

This was announced in 2010 by Cruciani et al. The majority of R-V88 was found in northern and central Africa, in Chadic speaking populations. It is less common in neighbouring populations.

The authors of Cruciani, et al. (2010) also found evidence of high concentration in Western Egypt and evidence that the closest related types of R1b are found in the Middle East, and to a lesser extent southern Europe. They proposed that an Eastern Saharan origin for Chadic R1b would agree with linguistic theories such as those of Christopher Ehret, that Chadic and Berber form a related group within Afroasiatic, which originated in the area of the Sahara.

The genetics make a quite strong case that Semitic languages are Southwest Asian in origin, probably Levantine, and that Chadic peoples have at least patriline genetic origins outside Africa and are relatively recent arrivals in Africa through male dominanted migrations seem quite convincing. But, this doesn't resolve the question of Afro-Asiatic linguistic origins, because the uniparental genetic markers don't point to a single common genetic origin for Afro-Asiatic language speakers across all of the subfamilies that make up the larger grouping.

Y-DNA Haplogroups T in Afro-Asiatic Linguistic Populations

There is also a good case that Y-DNA haplogroup T, found in a somewhat hard to characterize mix of populations including many Afro-Asiatic populations, is a backmigration to Africa from Southwest Asia. The Wikipedia survey of its frequency in Africa shows 26 instances of non-Afro-Asiatic peoples: 15 (of 256) in the Spanish Canary Islands that trace roots to North Africa, 6 (of 34) in the Bantu speaking South African Lemba who claim to have have Jewish roots, and 3 (of 17) of the Niger-Congo speaking Fulbe in Northern Cameroon right on the Afro-Asiatic and Niger-Congo population boundary in Africa, with the remaining seven instances involving three isolated cases in small Bantu populations, and four involving small percentages in Nilotic populations, each in samples mostly on the Eastern Coast of Africa which would have been exposed to Y-DNA T rich Somolians in the sea trade or near the Western boundary of Afro-Asiatic populations that are relatively rich in Y-DNA T. There were 108 from Afro-Asiatic populations.

Wikipedia on Haplogroup T also notes that:

Since haplogroup T is not associated with the R1, G and J lineages that entered Africa from Eurasia relatively recently, Luis et al. (2004) suggest that the presence of the clade on the African continent may, like R1* representatives, point to an older introduction from Asia.

The Levant rather than Southern Arabia appears to have been the main route of entry, as the Egyptian and Turkish haplotypes are considerably older in age (13,700 ybp and 9,000 ybp, respectively) than those found in Oman (only 1,600 ybp).

According to the authors, the spotty modern distribution pattern of haplogroup T within Africa may therefore represent the traces of a more widespread early local presence of the clade. Later expansions of populations carrying the E1b1b, E1b1a, G and J NRY lineages may have overwhelmed the T clade-bearers in certain localities.

Egypt, Ethiopia and Somolia are the dominant African locations of Y-DNA haplogroup T in Africa. The dispersal pattern of Y-DNA haplogroup T is far less clear cut than in Y-DNA R-V88 suggesting a deeper time depth. There are only a handful of instances apart from the Canary Islands, that are West of Egypt. It is not really a characteristic Berber marker (the one Berber population that showed it was in Lower Egypt and it was also found in Bengahzi near the Egyptian border with Libya). Instead, it marks Coptic, Cushitic and Omotic populations.

Y-DNA Haplogroups E1b1b in Afro-Asiatic Linguistic Populations

All of the Y-DNA T rich populations are also rich in Y-DNA E1b1b.

The Berbers, who lack much Y-DNA T, are even more rich in E1b1b.

On the other hand, E1b1b seems to have deep origins in Africa. Y-DNA haplogroup E is the dominant black African haplogroup (excluding Khoisan and Pygmy populations) where E1b1a (particularly associated with West Africa), E1a (particularly in West Africa and Sudan) and E2 (pan African, but especially Eastern and Southern Africa) are particularly common. There have been proposals for Y-DNA haplogroup E as back migrations, but I find them highly implausible.

Specific E1b1b subhaplogroups have associations with different groups. E1b1b1b (E-V257) is associated with Berbers. E1b1b1c1 (E-M34) is mostly Semitic. E1b1b1d (E-V6), E1b1b1f (E-V42), E1b1b1g (E-V92), and E1b1b2 (E-V16/E-M281) are all associated with Ethiopia. E1b1b1e* is found in Southern and Eastern Africa. Roots in Ethiopia or the vicinity seem likely.

Afroasiatic mtDNA Evidence

In contrast to the evidence from paternally inherited Y DNA, where Cushitic and Chadic linguistic populations have very different profiles from each other, a recent study has shown that a branch of mitochondrial haplogroup L3 links the maternal ancestry of Chadic speakers from the Sahel with Cushitic speakers from East Africa.

Other mitochondrial lineages that are associated with Afroasiatic include mitochondrial haplogroups M1 and haplogroup U6. Gonzalez et al. 2007 suggest that Afroasiatic speakers may have dispersed from East Africa carrying the subclades M1a and U6a1.

mtDNA haplogroups M1 and U6, and Y-DNA hapologroup R-V88 and J1 are back migrations from Southwest Asia when found in Africa, and there are also clearly distinctly non-African genetic signatures in Ethiosemitic language speaking populations. Ethiosemitic languages probably all have a common origin very early in the historic era.

Amar'utu Ul'iksuda

The blog Amar'utu Ul'iksuda, established just two days ago, has already caught my interest. Sixteen of the first nineteen posts are simply English translations of a variety of pre-monotheistic myths from around the globe, sometimes with a brief, non-argumentative preface. One post offers a brief summary of the bull mythology of Sumerian myth. The remaining two posts explore tersely intersections of myth with a role playing game, and with the Superman myth, respectively.

Despite the paucity of commentary from the author, the obscurity of some of the translated myths, the use of terminology usually used only by scholars, and the comfortable leaps to relatively advanced and academic concepts in the interpretive materials, suggest that the author is well read and has probably had some academic training in some kindred discipline. The author's profile also suggests a well developed interest in the esoteric and the mystical.

I look forward to seeing more.

Tuesday, March 13, 2012

Evidence For Demic Diffusion From mtDNA Restated

Mitochondrial DNA provide a genetic marker that is ancestry informative, matrilineal, and easier to extract and classify from ancient DNA samples than nuclear DNA. An accumulation of ancient DNA samples from European hunters and gatherer peoples (which pretty much ceased to exist as distinct populations ca. 2000 BCE), from early Neolithic populations (i.e. the first farmers of Europe), and from modern European populations, taken together, tell an important story that has been known for most of the last decade, with increasing certainty and is recounted in a recent academic journal article(references omitted):

In particular, 83% (19 out of 23) of hunter-gatherers analyzed to date carry mtDNAs belonging to haplogroup U and none of the hunter-gatherers fall in haplogroup H. In contrast, haplogroup U has been found in only 13 of 105 (around 12%) individuals from early farming cultures of Europe and it occurs in less than 21% of modern Europeans, while haplogroup H comprises between 25% and 37% of mtDNAs retrieved from early farming cultures and is in about 30% of contemporary Europeans. The mtDNA data thus suggest that the pre-Neolithic populations in Europe were largely replaced by in-coming Neolithic farming groups, with a maximum mtDNA contribution of around 20% from pre-Neolithic hunter-gatherers. . . . The high frequency of H-type mtDNAs in European Neolithic populations and its complete absence in pre-Neolithic hunter-gatherers suggests that H-type mtDNAs arrived with early farmers in Europe.

Estimates of the time frame in which a founding member of an mtDNA haplogroup that is survived by existing matrilines in Europe is calculated by making empirically estimated assumptions about how fast mtDNA mutation and counting back the number of mutations necessary to reeach a shared ancestor for a group of related mtDNA lineages. This dating methodology isn't perfect, but has performed much better, for a variety of technical reasons, than similar efforts to generate mutation rate dates from patrlineal Y-DNA.

The estimates of the genetic ages of related mtDNA lineages confirms the conclusion of the ancient DNA samples that mtDNA haplogroup H arrived in Europe with its first wave of farmers.

The population size increase observed between 9,000 and 5,000 YBP likely represents the population expansion that accompanied the Neolithic revolution. . .the H-type mtDNA population size seems to experience an exponential increase around 7,000 YBP, suggesting that both populations are not yet fused.

The more interesting contributions of the new paper are twofold.

First, it suggests that genetic diversity of Europe's hunter-gather populations dates only to the repopulation of Europe, following the Last Glacial Maximum, from refugia at lower latitudes in Europe, rather than having sustained the full range of genetic diversity dating from the pre-Last Glacial Maximum hunters and gathers of Europe in the Upper Paleolithic (ca. 40,000 years ago to 20,000 years ago, including the entire period of time when modern humans and Neanderthals co-existed in Europe), which was also a mtDNA haplogroup U dominated population so far as the small number of samples available to us can discern.

Second, the genetic and archaeological evidence coroborate each other in suggesting that between about 5000 BCE, when the first farmers arrived in a population that was largely from Europe's hunters and gatherers, and about 2000 BCE, when there ceased to be distinct hunter-gatherer populations in Europe, that the 20%-25% of the matrilineal gene pool of Europe that is there today had fully assimilated into to the gene pools of European farmers. For the most part, this fusion took place in the early Neolithic and Copper Ages of Europe, and predated Europe's Bronze Age.

In contrast, U-type mtDNAs show an increase in population size around 15,000 to 10,000 YBP, which coincides with the end of the last glacial maximum in Europe and a northwards expansion of hunter-gatherer populations. The data suggests that this population remained rather constant after 10,000 YBP until the onset of the Neolithic revolution. . . . After 4,000 YBP, no archaeological remains of hunter-gatherers were found in central Europe. From approximately that time on, both H- and U-type mtDNAs expand in a similar way. This may reflect fusion of the two populations where these mtDNAs were prevalent.

While I would argue that the data quoted above arguably support a pre-Neolithic hunter-gatherer contribution to the modern European genome of as much as 25% of Europe's gene pool, rather than 20%, the bottom line is that 75%-80% of Europe's matrilineal ancestors made their way into Europe either with its first farmers, or with later waves of migration.

Caveats and Implications

These conclusions come with some important caveats and implications.

1. Matrilineal ancestors are only a tiny percentage of any given person's ancestry. At a time depth of 2,500 years, someone has up to 2^100 ancestors, with many, in practice tracing multiple lines of descent to each individual alive today in the gene pool. But, there is no particular good reason to think that the statistical make up of all of the female ancestors in a population differs materially from the statistical make up of the matrilineal ancestory of a population.

2. The fact that particular individual has one mtDNA haplogroup or non-recombining Y-DNA haplogroup does not, standing alone, make that individual any more indigenous to Europe than someone else. You might fairly conclude that a whole group of genetically distinctive people who have high concentration of pre-Neolithic haplogroups will have a genetic makeup overall that is more similar to pre-Neolithic peoples of Europe. But, in populations that have even very modest genetic interaction with each other, over time, all genes without selective effects in the interacting populations will tend towards fixation, with each individual in the population tending over time to have particular genes from given source populations for the combined population that has reached genetic fixation of all of its genes similar to the relative genetic contributions of those source populations to the overall community at the start.

In other words, if 25% of maternal European ancestry is traceable to pre-Neolithic peoples of Europe, and 5% of paternal European ancestry is traceable to pre-Neolithic peoples of Europe, the odds are good that any particular European will trace 15% of the genes in their personal genome in a single one of their cells to the pre-Neolithic peoples of Europe, and that percentage is likely to vary to a surprisingly small degree within people in regions as large and larger than major regions within a modern European country.

Moreover, in general, the older a contribution to a gene pool is, the more likely that contribution is to have reached fixation and to have become simply one of random part of the mix that makes up some later gene pool into which the older contributing population to the gene pool has fused.

3. Generally speaking, matrilineal ancestry in a given place is more conservative than patrlineal ancestry in a given place. Mostly, this is because there is a recurring historical pattern of incoming men migrating into an area and having children with local women, in a way that increases their descendant's share of the gene pool relative to the descendants of local men. This implies that our default hypothesis, unless and until we have evidence to the contrary, is that less than 25% of the European paternal contribution to the modern European gene pool, possibly quite a bit less, is traceable to pre-Neolithic European hunters and gatherers.

4. While the literature isn't quite as well developed on this point, I think it is also plausible to suspect that admixture of small porportions of maternal ancestry may be more prone to gender asymmetry of genetic contributions than admixture of large proportions of maternal ancestry. This flows from the assumption that small percentages may arise from isolated instances of newcomers marrying local women, which is much less likely to happen to local men in ethnographically documented examples comparable to the situation of the first farmers of Europe. In contrast, large percentages are more likely to arise from wholesale assimilation of entire communities, which are more demographically balanced, into the society of the newcomers.

5. All other things being equal, a best first order estimate of the total pre-Neolithic European hunter and gatherer contribution to the European gene pool is roughly the average of the matriline and patriline contributions of pre-Neolithic European hunter-gatherers to Europe's modern gene pool.

6. The relative stablity of the matrline gene pool relative to the patriline gene pool, in historical examples, favors the hypothesis that R1b, the most common Y-DNA haplogroup in "Atlantic Europe" arrived with, or after, Europe's first farmers, and not before them.

Moreover, since Y-DNA haplogroup R1b is almost absence from ancient DNA from Europe's first farmers, the most plausible prediction is that it arrived on the European scene at high frequencies in the Copper Age or later, sometime in the last six thousand years or so. But, this is not a hypothesis that is easily tested with direct evidence from ancient DNA, because it is much harder to extract Y-DNA sample good enough to classify by haplogroup from the ancient DNA sources (particularly the interior parts of skeletal teeth) than it is to do the same with mtDNA.