Tuesday, June 30, 2015

Ancient DNA from the Carpathian Basin (5700 BCE to 3900 BCE)

A new study reviews ancient DNA results from six successive archaeological cultures from the terminal culture of pre-Neolithic hunter-gatherers to the middle Neolithic era in Western Hungary.  I was slightly influenced by it when writing my recent R1b post, but it deserves separate mention.

Bernard's blog provides the source data on mtDNA haplogroups, Y-DNA, the geographic context of the cultures, and PCA analysis based upon haplogroup frequencies.

While the results aren't paradigm busting, a few observations about the data are in order:

The Ancient DNA Sample

* There are a remarkable 336 ancient DNA samples in the study from which at least mtDNA results are obtained.  The data I've seen from the study do not discuss autosomal DNA, although it must be present for at least the samples from which Y-DNA haplogroups were obtained.

The Cultures

* There are six Neolithic cultures studied.  The earliest is Starcezo, which precedes the Vinca culture in essentially the same territory.  The Vinca culture, LBK culture, Sopot culture and Lengyel culture are neighbors geographically and essentially contemporaneous with each other.  The Vinca is the most Southeastern of the four contemporaneous cultures.  The Lasinja culture post-dates the Vinca, LBK and Lengyel culture and is contemporaneous with the late Sopot culture.  The Sopot culture is in a small area basically to the due north of the Vinca culture.

* Starcezo may be a first wave Neolithic culture, with the Vinca culture as the culture that follows after the first major farming bubble bust in the Neolithic era with a resurgence of hunter-gatherer DNA.  Alternately, the resurgence of hunter-gatherer DNA in Vinca samples may be due to the "economic stresses caused by decreasing soil fertility" after two millennia of intensive farming that this culture itself experienced in its declining years.  But, the Neolithic cultures further north and west don't experience the same resurgence of hunter-gatherer population genetics.

* Historically, there has been debate in anthropology between those who see Vinca as a local evolution of Starcezo, and those who see it as a result of migration from Anatolia.  The genetic data seems to favor the former scenario, but suggests that the LBK, Sopot and Lengyel cultures may involve more new migration from Anatolia or elsewhere.

* The Vinca culture is notable as one of the earliest in which proto-writing and commercial seals, similar to those found in the Harappan civilization, appear in Europe and pre-dates the use of the Indus Script of the Harappan civilization by more than 700 years (seals were also used in the Copper and Bronze Age civilization of Anatolia, Sumeria, Assyria and Egypt).  Per Wikipedia on Vinca culture:
The Vinča culture occupied a region of Southeastern Europe (i.e. the Balkans) corresponding mainly to modern-day Serbia, and Kosovo, but also parts of Romania, Bulgaria, Bosnia, Montenegro, Macedonia, and Greece. This region had already been settled by farming societies of the First Temperate Neolithic, but during the Vinča period sustained population growth led to an unprecedented level of settlement size and density along with the population of areas that were bypassed by earlier settlers. Vinča settlements were considerably larger than any other contemporary European culture, in some instances surpassing the cities of the Aegean and early Near Eastern Bronze Age;a millennium later. One of the largest sites was Vinča-Belo Brdo, it covered 29 hectare and had up to 2,500 people.

* All 19 of the hunter-gatherer samples have one of five different mtDNA U haplogroups (counting 2 mtDNA U not further specified due to degradation of the sample as a separate category).

* All of the Neolithic samples have substantial mtDNA diversity (at least six or more mtDNA top level haplogroups represented).  At least some Neolithic sample has examples of mtDNA not found in the hunter-gather sample including H, HV, V, J, K, N1a, T1, T2,  U3, U8, W and X.  This tends to suggest that at least the maternal origins of the first wave Neolithic peoples of Europe were part of the culture that fused populations that before the Neolithic revolution were distinct into a melting pot whole.  As I note below, there was far less Y-DNA diversity, a fact that casts some doubt on the anthropological conception of the archaeological cultures of "Old Europe" as matrilineal.

* A quite significant share of the Vinca samples are also mtDNA U (about 22.5%), but it is quite rare in the other Neolithic samples.  This is a resurgence in mtDNA U frequencies from the previous Starcezo culture.

* There is a significant mtDNA mix difference between Starcezo and Vinca on one hand, and the other Neolithic cultures, including a significantly higher frequency of mtDNA H in the other cultures, and a significantly lower frequency of mtDNA U in the other cultures.  The Starcezo culture has only 6.9% mtDNA H and the subsequent Vinca culture has even less, but the levels of mtDNA H are much higher in the other Neolithic cultures in the sample (LBK, Sopot, Lengyel and Lasinja), which have percentages of mtDNA H from 16.67% to 28.54%, still lower than modern levels, but much higher than Starcezo and Vinca.


* There is no hunter-gatherer ancient Y-DNA in the sample.  Elsewhere in Europe, ancient hunter-gatherer Y-DNA has almost universally been haplogroup I1.

* The Neolithic samples (pre-Bronze Age) include Y-DNA G2a, F*, I2, E-M78, J2 and surprisingly C.  There is also one sample of Y-DNA I1 from the LBK culture (possibly representing a hunter-gatherer male integrated into farmer society at some point).  There are Y-DNA samples from all six of the Neolithic cultures studied.

It bears noting that this is not a "Near Eastern" mix, a description often ascribed to the genetics of first farmers in Europe.  Y-DNA G2a, F* and J2 are what we would expect from a source in Anatolia or the Caucasus Mountains or the highlands of Iran, not the Levant or Arabia or even the lowlands of Mesopotamia (although J2 would surely be found in Mesopotamia in significant proportions).  Y-DNA I2 suggests Paleolithic variation in European hunter-gatherer populations that happened to crop up in the Balkans (and later re-emerged as a post-Nordic Neolithic revolution Scandinavian Y-DNA clade).  Y-DNA E-M78 is the only Y-DNA clade in the first farmer population of Europe that evokes Near Eastern origins and this makes up only about 6.67% of the Neolithic ancient Y-DNA population sample in this study and could have been picked up by the populations where it is found en route from their place of origin to the places that they settled in Europe in the Neolithic era.

The first European farmers probably emerged from the highlands that form the Southern boundaries of Europe and West Asia, rather than from what we would conventionally think of as the "Near East" proper.

* The Starcezo and Vinca culture combined have 4 examples of Y-DNA G2a, 3 of F*, and one of I2a1.  The absence of Y-DNA E-M78 is notable, because this is present at quite high levels in the part of Europe where the Vinca culture was present.  Instead, the two E-M78 samples in the study come from further north, where E-M78 is found only in moderate frequencies today.

* But, one shouldn't read too much into a sample size of just eight men, when other evidence suggests that there is more to the story.  If the N=8 sample were random and independent (which it isn't) a proportion of Y-DNA E-M78 in the Neolithic era as E-M78 of about 33% (the peak modern European percentage found in Albania) is just barely ruled out at the 95% confidence level, and moderately lower modern proportions of E-M78 in the Starcezo and Vinca regions are not excluded in a statistically significant way.  A Neolithic proportion of E-M78 of 17% for example, would be perfectly consistent with a failure to find any samples of it in a sample size of N=8 which is random and independent (which these samples are not).

The Starcezo and Vinca cultures are in just the right place at just the right time to be the source of the high levels of Y-DNA E-M78 in the region in modern Europe (and for that matter as the place where the E-M78 introgressed into other early Neolithic culture's gene pools).  The explosion in the regions population relative to the Starcezo culture upon the appearance of the Vinca culture's much more successful agricultural society, also creates a moment in time where founder effects might cause a moderate underlying level of E-M78 (and in particular, E-V13), to be dramatically amplified relative to the Starcezo background in a way that would leave a permanent imprint on the region's population genetics.

Everything we know about Bronze Age migration into the region disfavors that migration period as a major source of E-M78 in this region.  So, one is left between a choice of a Neolithic source and an Iron Age or later source for this part of the Y-DNA gene pool in the Balkans.  In the latter scenario, perhaps E-V13 arrived in the Balkans during the time period when it was part of the Ottoman empire, since some accounts assert that there was significant population replacement and mass resettlement of Ottoman populations into its borderland. But, given the antiquity of E-M78 in Europe (e.g. in a 7000 year old Spanish individual), the Neolithic possibility still seems more likely, despite the lack of Hungarian ancient DNA to support this hypothesis in this small sample.  The Neolithic theory also has support from the time depth of the E-V13 subclade of E-M78 which is the predominant Y-DNA E clade in the Balkans of about 8,100 years ago, right around the time of the Neolithic revolution and the Vinca population explosion there.

UPDATE (July 2, 2015): Wikipedia recalls a literary reference that could be relevant to the question of Y-DNA E in the Balkans:
In Aeschylus's play, The Suppliants, the Danaids fleeing from Egypt seek asylum from King Pelasgus of Argos, which he says is on the Strymon including Perrhaebia in the north, the Thessalian Dodona and the slopes of the Pindus mountains on the west and the shores of the sea on the east; that is, a territory including but somewhat larger than classical Pelasgiotis. The southern boundary is not mentioned; however, Apis is said to have come to Argos from Naupactus "across" (peras), implying that Argos includes all of east Greece from the north of Thessaly to the Peloponnesian Argos, where the Danaids are probably to be conceived as having landed. He claims to rule the Pelasgians and to be the "child of Palaichthon (or 'ancient earth') whom the earth brought forth".

The Danaids call the country the "Apian hills" and claim that it understands the karbana audan (accusative case, and in the Dorian dialect), which many translate as "barbarian speech" but Karba (where the Karbanoi live) is in fact a non-Greek word. They claim to descend from ancestors in ancient Argos even though they are of a "dark race" (melanthes ... genos). Pelasgus admits that the land was once called Apia but compares them to the women of Libya and Egypt and wants to know how they can be from Argos on which they cite descent from Io.

In a lost play by Aeschylus, Danaan Women, he defines the original homeland of the Pelasgians as the region around Mycenae.
The original legend is also set out more fully here, where it is notable that Pliny the Elder;s "Natural History" is another source for the legend, and it is conjectured that:
Even a cautious reading of the subtext as a vehicle for legendary history suggests that a Pelasgian kingship in archaic Argos was overcome, not without violence, by seafarers out of Egypt (compare the Sea Peoples), whose leaders then intermarried with the local dynasty. The descendants of Danaus' "blameless" daughter Hypermnestra, through Danaë, led to Perseus, founder of Mycenae, thus suggesting that Argos had a claim to be the "mother city" of Mycenae.
Naively, this story suggests that rather than being European hunter-gatherers who were assimilated into the first wave of Neolithic farmers in the Balkans, that the Pelasgians may have been the first wave Neolithic farmers in the Balkans (who probably arrived ca. 7000 BCE-6000 BCE), and that a Y-DNA E-M78 people called the Danaids arrived in a post-Neolithic folk migration from Egypt or Libya after the Pelasgians were established, but before the arrival of the Indo-European Greeks (who probably started to appear around 2000 BCE).  The fact that this migration was not lost to the tradition when Aeschylus was writing in classical Iron Age Greece, and that Egypt may have been a meaningful polity at the time, suggests that the Danaids may have arrived in the Eneolithic era (i.e. Copper Age) ca. 4000 BCE - 2000 BCE in this part of Europe.

The comparison to the Sea Peoples (who are associated with Bronze Age collapse ca. 1200 BCE and some of whom were ethnically Indo-European Greek), however, poses the intriguing possibility that there may have been a similar phenomena in the wake of the similar empire felling climate event around 2000 BCE, placing the Danaids in a very specific time and place indeed, and having them arrive on the scene very shortly indeed before the arrival of the Mycenians whose language become Ancient Greek, just as in the narrative.

Obviously, legendary history alone shouldn't be taken at face value, but Aeschylus gives us a general time frame and a very specific geographical pointer regarding where to look for archaeological evidence that the Danaid migration ever happened.  One could point to a pyramid like structure in Argos whose age and interpretation is disputed as a sign of an Egyptian connection to Argos though the Danaids. END UPDATE.

* Y-DNA R1b does not appear until the Bronze Age, where there are 2 Y-DNA R1b samples and there is one Y-DNA I1 sample.  The study does not appear to include Bronze Age ancient mtDNA samples.  Naively, I would have expected Y-DNA R1a rather than R1b in the Bronze Age this far to the east in Europe.  Could it be that R1b made its way to Western Europe via the Balkans and then across the Southern part of Europe to Iberia, perhaps originating in the Yamnaya people?

As Maju has noted at this blog and in comments on one of my recent posts, it isn't sufficient to look merely at crude top level Y-DNA clades to resolve these questions, because what may look the same at gross level, may imply an impossible phylogeny when more detailed Y-DNA clade descriptions are considered.  We are looking for a trail of parent to daughter clades from East to West until you get to the root of Western European Y-DNA R1b clades.

As noted above, small samples can be misleading, but the total absence of any Y-DNA R in any of the 30 pre-Bronze Age samples from the region, while it may not rule out the possibility that there was some Y-DNA R in the region during the Neolithic, does seriously disfavor the possibility that Y-DNA R was present at anything approaching its modern frequency in the region during the Neolithic era.  Modern populations in this region have from 20%-60% Y-DNA R1, with significant amounts of both R1a and R1b in almost all of these populations.

If the N=30 sample were random and independent (which it isn't) a proportion of R1 in the Neolithic era or more than about 10% is disfavored at the 95% confidence level, and the expected proportion of R1 would be not more than about 5% given the data in the sample that we do have and ignoring our Baysean priors from our wider knowledge of ancient DNA.  The nature of sample size statistics is that even the slight improvement from N=8 to N=30 dramatically improves statistical power, even though this improvement shows diminishing returns as N increase (to the point where, for example, the difference in statistical power between a sample size of 800 and 3000 is quite modest).

Also, knowing what I know now about the fact that Slavic peoples made their way into the Balkans from the North and had a significant demic component (unlike many other migration period "barbarians"), it isn't implausible that at least some of the Y-DNA R1a in the Balkan region today arrived as late as the Iron Age from Slavic migration (which would have predominantly Y-DNA R1a relative to Y-DNA R1b), and that the ratio of R1b to R1a in the Balkan region was higher in the Bronze Age than it is today.  And, the R1b blending proportions with R1a in the Balkans, unlike in many other parts of Europe, is not a good fit to historical boundaries between the Bell Beaker cultural area and the Corded Ware cultural area that succinctly describes the relative proportion of these Y-DNA types in most of Europe.  So there is a window in time in the Bronze Age during which R1b could plausibly have been dominant in a population that migrated through Western Hungary on to Western Europe.

Monday, June 29, 2015

Y-DNA E Better Understood

A new study of the phylogeny of Y-DNA E (via Bernard's blog) shows more regionally defined structure of different subclades of the Y-DNA haplogroup than had previously been discerned, particularly in Eastern and Southern Africa.

It also provides a wealth of data on the time depth of various Y-DNA E subclades, although given the wide disparities that exist in establishing mutation rate dates, this is more useful in terms of establishing relative ages than absolute one.

The study puts the split of Y-DNA D and Y-DNA E at 69,000 to 69,800 years ago.

Y-DNA E-M81, which is the predominant Berber clade (also found in moderate frequencies in Iberia, in Turkey and in Bedouins, and at low frequencies in Italy), breaks off from the clade that includes my own Y-DNA E-V13 (which is found in high frequencies in the Balkans and moderate frequencies in much of the rest of Europe and Turkey and among the Druze) between 24,100 and 25,000 years ago, around the time of the Last Glacial Maximum.

E-M81 probably arrives in Europe via the Strait of Gibraltar, in the Mesolithic or early Neolithic era, with an additional significant influx to Moorish Spain in the last 1,300 years.

E-V13 probably arrives in Europe via the Levant and disperses from there to the rest of Europe at roughly the same time or perhaps a bit later, around the Mesolithic or Neolithic era (mutation rate dating puts the origin of this clade at about 8,100 years ago).  Ancient DNA from clade E-M78 (which is a parent of E-V13) is found in Iberia ca. 7,000 years ago and Y-DNA clades that are part of the E-M78 clade are present in Iberia in similar frequencies to E-M81.  The spread of E-V13 to the Balkans and its expansion there must have happened sometime in pre-history, because no known historical migrations prior to first wave Neolithic migrations could account for its strong presence in the Balkans.

While a number of individuals have argued for an Eurasian origin for Y-DNA E, based on the fact that its sister clade Y-DNA D is predominantly found in Asia, an examination of the phylogeny of Y-DNA E together with the geographic distribution of its currently known branches argues strongly for an African origin for Y-DNA E, rather than a Eurasian one, as do other factors such as the presence of individuals with Y-DNA DE not further distinguished between D or E in both Tibet and Africa.

Many relatively basal branches of Y-DNA E are found almost entirely in Africa and the African diaspora (e.g. African-Americans and Afro-Caribbean populations), while only a couple of relatively young branches of Y-DNA E are found (mostly at moderate frequencies) in parts of Europe and the Near East adjacent to Africa. See, e.g., page 4 of the supplementary materials for the new study. Those branches of Y-DNA E found outside Africa, moreover, are related to each other only via branches of Y-DNA E found only in Africa.

As Wikipedia notes:
E1a and E-M75 are found almost exclusively in Africa. By looking at the major subclade frequencies, five broad regions of Africa can be defined: East, Central, North, Southern and West. The division can be distinguished by the prevalence of E-V38 in East, Central, Southern and West Africa, E-M78 in East Africa and E-M81 in North Africa. E-V38 is the most prevalent subclade of E in Africa. It is observed at high frequencies in all African regions except the northernmost and easternmost portions of the continent. E-M243 (especially its subclades M78 and M81) is found at high frequencies in North East Africa and North Africa and is the only subclade that is found in Europe and Asia at significant frequencies. E-M243 is common among Afro-Asiatic speakers in the Near East and North Africa as well as among some Nilo-Saharan and Niger–Congo speakers in North East Africa and Sudan. E-M243 is far less common in West, Central, and Southern Africa[.]
It is also unlikely that Y-DNA had origins in Northwest, West, Central or Southern Africa. E-V38, which is most common in these regions, according to the new study, mostly expanded and diversified in the last 15,300 years, making it the youngest major branch of Y-DNA E. Y-DNA E diversity also tends to decline from East to West across North Africa. Instead, East Africa is the likely place of origin of Y-DNA E.

Ethio Helix has some solid analysis of the new data, although his page is hard to read in some browsers.  In particularly, he notes that the study localizes the older part of one of the main branches of Y-DNA E in Northern Ethiopia and Sudan.

Wednesday, June 24, 2015

Parasites and the Rise and Fall of Empires

John Hawks notes the possibility that widespread parasite infestation in a particular region could make it vulnerable to conquest by another group of humans without that infestation.

The quoted passage cites no documented historical examples of this happening, but it is worth putting into the mix of possible causes of the rise and fall of ancient (and not so ancient) empires.

Tuesday, June 23, 2015

More Ancient DNA!

Via Eurogenes (emphasis added):
The Y-chromosome belongs to macrohaplogroup F and the mtDNA to macrohaplogroup N. For details see the supp info PDF here. The full paper is freely available here.

Qiaomei Fu et al., An early modern human from Romania with a recent Neanderthal ancestorNature(2015) doi:10.1038/nature14558
Abstract: Neanderthals are thought to have disappeared in Europe approximately 39,000–41,000 years ago but they have contributed 1–3% of the DNA of present-day people in Eurasia. Here we analyse DNA from a 37,000–42,000-year-old modern human from Peştera cu Oase, Romania. Although the specimen contains small amounts of human DNA, we use an enrichment strategy to isolate sites that are informative about its relationship to Neanderthals and present-day humans. We find that on the order of 6–9% of the genome of the Oase individual is derived from Neanderthals, more than any other modern human sequenced to date. Three chromosomal segments of Neanderthal ancestry are over 50 centimorgans in size, indicating that this individual had a Neanderthal ancestor as recently as four to six generations back. However, the Oase individual does not share more alleles with later Europeans than with East Asians, suggesting that the Oase population did not contribute substantially to later humans in Europe.
The ability of science to present this evidence is absolutely stunning.  The lack of a West Eurasian v. East Eurasian genetic leaning more than 10,000 years into the Upper Paleolithic, despite lacking any private East Eurasian Y-DNA or mtDNA haplogroups, is surprising.  This also brings to mind the fact that none of the Y-DNA samples of European hunter-gatherers has Y-DNA D or E.

Also via Eurogenes, is the paper below, which analyzes a limited reconstruction of a Neolithic individual from what is today Barcin, Turkey:
Pinhasi R, Fernandes D, Sirak K, Novak M, Connell S, Alpaslan-Roodenberg S, et al. (2015) Optimal Ancient DNA Yields from the Inner Ear Part of the Human Petrous Bone. PLoS ONE 10(6): e0129102. doi:10.1371/journal.pone.0129102
A PCA analysis places the sample near Sardinians, but shifted in the direction of Near Easterners.  Another analysis shows Sardinians, Italian Tuscans, Basque, Turkish Jews, and Western Ukrainians all fairly close.  An ancestral component analysis concludes that:
The lack of Ancient North Eurasian (ANE) ancestry isn't surprising, because it mirrors the results of early European farmers we've seen to date.  
Moreover, the relatively high level of Western European Hunter-Gatherer (WHG) ancestry, or at least something very similar, is also in line with expectations, considering that the sample was dug up in far western Anatolia, almost on the European border. 
Bottom line: Neolithic Western Anatolians look a lot like other first wave Neolithic farmers, confirming the leading paradigm of demic migration in the first wave of the European Neolithic.

Monday, June 22, 2015

Lubos Plays Dumb On Non-Locality In Quantum Entanglement

Lubos makes a big fuss at this blog arguing that the correlation of quantum properties of particles that were previously entangled at a common point does not constitute non-locality and that people who believe otherwise are "anti-quantum zealots" (and more particularly in response to this post which starts on the right course but then starts to get weird at about the third paragraph past the second video clip).

Lubos does so by defining "local" phenomena as acting on particles that are in the same light-cone from their common origin (i.e. that a decision that is at space-like separated point from a measurement can't influence the measurement), and stubbornly refusing to acknowledge that this is a far broader definition than most people who talk about non-locality in quantum mechanics mean. For example, he succinctly sums up his definition of "local" when he states:
When I say that the entanglement always and exclusively exists when the two subsystems have a common origin, it's important to realize "where this claim comes from" and "why we know it's right". It's right because:
1. it follows from the locality of the quantum field theory etc. at the beginning: a sudden creation of correlated bits at spacelike-separated points could be used to send information instantaneously, and that would violate locality (which can be mathematically proven to be impossible)
2. this fact is also compatible with all the experiments that have ever been done.
While surely this is a true statement, the mere fact of having a common origin is normally only considered proof of locality, in the usual sense of the word, if the ultimate outcome of the measurement, and not merely their correlation, (a concept that I call "fate") is determined at the time that the particles have a common origin.

Normal people discussing non-locality, mean that measuring one formerly entangled particle allows you to know with certainty, something about the properties of the other particle whenever it happens to be measured, even if the particles are some distance apart from each other at the time of measurement and that the outcome of whichever measurement took place first (for example, in proper time relative to the point of entanglement) was not predetermined at the time of entanglement.

But, it isn't obvious that "fate" is what is going on in the quantum mechanics of entangled particles. If the outcome of the measurement is truly still indeterminate at the point in space and time of common origin (which is what we usually assume in quantum mechanics for good reason), then the correlation does not fit any conventional definition of non-locality in the case of entangled particles.

The definition of causality that Lubos uses is more conventional: "The relativistic locality ends up being equivalent to the relativistic causality: the cause must precede its effects, t is less than t′, in all inertial systems."  The would preclude what I call the Feynman explanation of information going backward in time from the point of measurement, and then forward in time from the point of entanglement (even though this isn't necessarily inconsistent with Lorentz invariance, because photons and other massless particles travel at the speed of light and don't experience the passage of time "subjectively"; everything in the path of a photon or other massless particle in a light-cone happens simultaneously in the reference frame of the massless particle, so causality isn't a meaningful concept from its perspective).

The probability that any measurement made in isolation will take a particular value, however, is perfectly random.

One possibility is that the values that the entangled particles will take when they are ultimately measured is "fated" at the time of entanglement, even though it won't be learned until much later. This seems inconsistent with the general notion in quantum mechanics (established in many other contexts) that quantum mechanical measurements are indeterminate until measured and that an unmeasured set of probabilities for a quantum system before measurement differs from a measured quantum system.  (Sometimes this is called the question of "reality").  The notion of "hidden variables" is similar although not necessarily identical.

The notion that Bertlmann's socks are anti-correlated (i.e. different in color) whenever they are measured because he always picks two opposite colored socks at the start of the day at some point, fits with the idea that the outcome you will get is predetermined at the time of entanglement even though, so that even though you have no way of knowing which sock you will measure in advance (making the probability of picking one or the other perfectly random), the answer was predetermined when that sock started on its path to being measured, as we the answer to the color of the other sock when it started on its path to being measured.  The outcome of the measurement existed at the time that the entangled particles separated, even though it was not known until later.

Another possibility is that the values that the entangled particles will take when they are ultimately measured is determined at the time of the first measurement and "communicated" instantaneously when the other particle is measured (implying a superluminal exchange of information).  This what is commonly called "non-locality" by people discussing the subject.

A third possibility is that the values that the entangled particles will taken when they are ultimately measured is determined at the time of the first measurement and "communicated" by a message that goes backward in time to the point of entanglement and then forward in time to the other particle when it is ultimately measured.  This is what is commonly called a "causality" violation by people discussing the subject (because causality implies that information travels only forward in time).

It is called a "paradox" because if hidden variables and non-locality and acausality are all not true, then how this happens doesn't fit in our classical physics trained brains.

In a key passage he states:
All this confusion began with the flawed 1935 paper by Einstein, Podolsky, and Rosen. Einstein and the two postdocs were thinking in the classical way and they found it unbelievable that the correlations could exist for all the components j⃗ ⋅n⃗ simultaneously.

They thought that if the two electrons are guaranteed to have anticorrelated values of jz, they objectively have to exist either in the state |↑↓⟩ or the state |↓↑⟩ before the measurement. But because both |↑⟩ and |↓⟩ predict 50% probability for jx=+1/2 and 50% probability for jx=−1/2 and this "split" applies to each electron, EPR and their followers found it "necessary" for the probabilities of j1x,j2x to be either "positive,positive" or "positive,negative" or "negative, positive", or "negative,negative" to be 25%, 25%, 25%, 25%, respectively.

However, that's simply not what quantum mechanics predicts. Everyone who understands quantum mechanics agrees that the perfect anticorrelation will exist if we measure j1x and j2x, too. The wrong assumption in the EPR derivation is classical physics. They assume that the two spins already have some independent well-defined states before they are measured. But they don't. Before they are measured, the two spins are entangled – which is nothing else than the most accurate and most general quantum elaboration on the adjective correlated.

The correlations between the results of measurements is a correlation. The previous sentence is a tautology. There are still some people who try to pretend that the correlation is something else than a correlation even though they use the word "correlation" themselves. We say that the measurements of the two electrons are correlated because the probability distribution p(j1x,j2x) for all four possible arrangements of the values of j1x and j2x does not factorize: 
The full probability distribution for the two objects (electrons' spins) simply cannot be written as a simple product of two distributions for one object (for the objects separately).

Assuming the initial singlet state, quantum mechanics predicts these correlations for all the spin measurements you can think of. There is nothing "paradoxical" about it. There isn't any classical theory (or a "classical model") that makes the predictions. This fact isn't a problem with quantum mechanics or a mystery about quantum mechanics; instead, this fact is a proof that all classical theories are ruled out as theories of Nature. They are wrong. People who keep on defending them may be easily proven to be complete idiots. That's obviously the only right interpretation of the result.

What is the reason of these correlations? According to the right theory – quantum mechanics (e.g. quantum field theory where this EPR experiment may be easily embedded), the reason of the correlation(s) is not an action at a distance. At the beginning, I reminded you of the proofs that there is no action at a distance in quantum field theory!

Instead, the reason of all these correlations – the reason of the entanglement – is the two subsystems' being in the contact in the past.
Lubos is basically arguing that the equations of quantum mechanics tell us how reality behaves and that we shouldn't need to try to impose any further interpretation upon it, and that trying to ask the question of the mechanism by which quantum entanglement produces anti-correlations is essentially a category error. But, he also argues stringently that non-locality and acausality are not involved, which makes it feel like he is arguing for the "fate" version of the options, even though that overstates somewhat what he is really saying.

Indeed, he hedges in this paragraph:
The same comment applies to the anticorrelation of the spins in the singlet state. They're anticorrelated because they were prepared together. In the ER-EPR correspondence, this anticorrelation (or any entanglement) may be interpreted as a non-traversable wormhole. But such wormholes have to be created locally i.e. have a common origin, too. You create the two "throats" of the Einstein-Rosen bridge and then you may increase the distance between them. But there's no way to "suddenly" create a bridge between two spacelike-separated points!
In other words, he's basically acknowledged both a "fate-like" interpretation with the correlations arising in the past at the time of entanglement, and a "non-local" non-traversible wormhole interpretation so long as the wormhole has to be created locally, are interpretations consistent with observation.

Nobody is actually seriously arguing that entanglement can arise without a common point of contact, a straw man that he argues against that is indeed contrary to scientific fact.

The argument that one is talking about a category error could arise one of a couple of ways.  First, if there is not even in principle any way to distinguish different interpretations of what is going on in entanglement, then it would seem that one is asking a nonsensical question.

Second, if we have a true paradox where any proposed interpretation leads to a logical contradiction, then we again we seem to have asked a nonsensical question, although in that case the question of which of our assumptions is wrong comes to the fore, and the problem is that canonically two of our three assumptions may be wrong and yet reach the right answer, but again, it isn't obvious that there is any way to do experiments that consistently tell us that one assumption and not another, is incorrect.

The Bohmian formulation of quantum mechanics tries to use a "fate-like" interpretation.

Richard Feynmann, when he was explaining quantum mechanics to the public, tended to favor explaining the "acausal" approach in which information could travel both forward and backward in time.  I tend to favor this description because:

1.  It emphasizes that quantum mechanics does not itself have an arrow of time and treats space-like and time-like separations essentially identically.  You can rotate the space-time coordinates of a Feynmann diagram and still have quantum mechanically equivalent statements.

The lack of a fundamental arrow of time in quantum mechanics, and Feynman's notion of antiparticles as particles traveling backward in time, also has potentially great utility in explaining the matter-antimatter asymmetry in the universe.  My conjecture on this point is that anti-matter goes backward in time from the Big Bang (or much less commonly, from points after the Big Bang when it is created/annihilated depending upon your point of view), and ordinary matter matter goes forward in time.  Photons, which are timeless, go in both directions at once.  Thus, there is an absence of anti-matter in our universe, because most of the anti-matter created around the time of the Big Bang is in a parallel universe before the Big Bang in which time runs in the opposite direction.  Feynman's characterization of anti-matter solves this cosmological mystery elegantly, with matter-antimatter pairs that are on opposite sides of the event horizon of the Big Bang, without the need for violations of baryon number or lepton number sufficient to explain the matter-antimatter asymmetry that we observe which is otherwise far too great to explain within the context of Standard Model sphalerons.

2.  It emphasizes the pre-measurement indeterminacy of quantum mechanical objects (illlustrated, for example, by double slit experiments) which is of such importance for a variety of purposes in quantum mechanics, that it makes sense to believe may be rightly considered to be a general rule.

Now, if one of the particles is measured long in time before the other, you have some of the same issues as predetermination at the time of entanglement.  But, perhaps the timelessness of the photon or massless communication of information in the information carrier's frame of reference eliminates these concerns.

3. It maintains the principle of locality in the stronger sense that I have defined, rather than merely in the weaker sense (existence in the same light cone from a point of common origin) that Lubos prefers to use.

Also, the mere fact that something doesn't contradict the laws of science, doesn't mean that a scientific reality that is wildly contrary to intuition isn't remarkable and worth a lot of discussion about its meaning, since that goes to the meaning of the universe itself and our assumptions about it.

Improving Our Understanding of R1b in Western Europe

Maju analyzes some new data on predominantly Western European clades of Y-DNA R1b and fits that into a working hypothesis based on the larger picture of R1b distributions in West Eurasia.

In a nutshell, it appears that R1b-S116 expands into three different daughter clades in three directions from somewhere in the vicinity of central France, one to Normandy and the British Isles, one to Central Europe and the Alps, and one to the Southeast (especially Iberia).

R1b-S116, in turn, could have origins in Iberia via Southern Italy, or in Central Europe, or both in parellel routes to central France.  These way stations could in turn come from R1b-M269 in the Balkans or Highlands West Asia (e.g. including Iran).  The answer to this question (when and where this happened) is one of the hottest questions in European archaeogenetics, because it is in furtherance of the goal of determining the archaeological culture(s) which were involved in this massive genetic transmission of the dominant Y-DNA clade today in Western Europe to its current location.  To answer this question is to unveil the face of the patrilineal ancestors of most Western European men.

Maju figures that from where ever the launching point might be that the most basal R1b would have its ultimate origins in West Asia.  This seems plausible enough, with R2 centered in South Asia and Western Iran, particularly in the Indus River Valley which is mostly Pakistan today, and R1 found in Iran and much of Europe and Central Asia, as well as appearing in South Asia in close correlation with hypothetical Indo-Aryan invaders (particularly R1a).

But, the fact that R1a and R1b were both present and bifurcated on the Russian steppe in the Mesolithic era, along with ancient DNA that seems to point to the Altai is the deeper place of origin for the entire Y-DNA R clade, suggests that West Asia may have received R2 from the steppe, during the Paleolithic era, rather than the other way around, with R1a and R1b arriving later in the Copper Age or early Bronze Age by different routes.  It is hard to distinguish between the scenarios given the available data.


Recent ancient Y-DNA studies put examples of Y-DNA R1b and R1a on the European Steppe by the early Bronze Age or even a few centuries earlier.

In particular, European hunter-gatherer populations in Russian have ancestral Y-DNA R1 to the herders and farmers who subsequently live there, suggesting that the spread of R1 to the Russian steppe was

Corded Ware people, as expected, are predominantly R1a and have origins to the North of the Yamnaya people.  The story of R1a in Europe, to quote Eurogenes, can be summed up as follows:
- Mesolithic Hunter-Gatherer from Karelia: R1a (xM198)

- Late Neolithic Corded Ware pastoralist from Germany: R1a (M198, M417, xZ282)

- Late Bronze Age Urnfielder from Germany: R1a (M198, M417, Z282, Z280).
The Corded Ware people and their successors were almost surely Indo-Europeans.

The story of R1b is complicated, however, and the question of how R1b got to Western Europe remains more cryptic.

For example, Tarim Basin mummies are R1a, but the Yamnaya people, the hunter-gatherers from the area where the Yamnaya culture emerged (the Samara Valley), and the Afansievo people are R1b. This means that the Yamnaya and Afansievo people are unlikely direct ancestors for the Tarim Basin mummies, despite the fact that the Afansievo people arrived nearby before the Tarim Basin culture arose.  It suggests a more Northerly route of arrival for the Tarim Basin people, or a later one, as the Indo-Iranians are predominantly R1a.

All ancient Bell Beaker Y-DNA to date are R1b, but the sample to date isn't very representative and is limited largely to Germany, while missing core areas where the Bell Beaker culture was found,

The modern distribution of R1b in Europe, however, is a decent fit to the range of the Bell Beaker culture (with declining frequencies in places where it was more marginal).

Importantly, as well, the Basque are very high in R1b, suggesting strongly that R1b was brought to Western Europe by people who were not Indo-European linguistically and that Indo-European languages only arrived in Western Europe with the Celts or realistically, with their predecessor Urnfield people whose language was probably the source of both the Italic and Celtic languages.  In other words, Indo-European languages arrived in Western Europe only around the time of Bronze Age collapse.  (A similar argument for an origin of Germanic languages in Northwestern Europe around the time of Bronze Age collapse is also consistent with the evidence.)

Taken to its logical conclusion, if the Yamnaya people are the forebears of the Bell Beaker and other Western European Y-DNA R1b peoples, and while the Corded Ware people are the forebears of the European R1a people, the Yamnaya people may not have been Indo-Europeans after all.  Instead, they could very well have been linguistically Vasconic (i.e. linguistically in the same family as the Basque language).

As Dienekes notes, the data tend to show that "the later steppe cultures of the Sintashta and Andronovo (putative Indo-Iranians according to some), were not a continuation of the Yamnaya-Afanasievo people," as had been widely assumed before the ancient DNA data was available. Dienekes also notes genetic continuity between modern Armenians and those of the early Bronze Age.

As Maju notes, it isn't clear if R1b took a continental route, Mediterranean route, or both, to Western Europe from an origin in Southeast Europe and/or West Asia.

Maju demurs on the timing of R1b's arrival, but suggests that Atlantic Megalithic as well as Bell Beaker were likely involved, rather than a later arrival with Bell Beaker people alone.

New Experiment Tends To Confirm Electron-Muon Universality

In the Standard Model, electrons and muons are assumed to have all of the same properties except mass.  This is called lepton universality.

Some recent experimental results from the LHC involving B meson decays have shown seemingly statistically significant deviations of electron-muon universality, with decays from the same source particle producing statistically significant differences in the number of decay products with electrons, from the number of decay products with muons, when they are predicted to be the same subject to adjustments based upon the relative masses of the particles (at roughly a 2.6 standard deviation level before considering look elsewhere effects).

Those results, while not very interesting in isolation, seemed notable because of two other anomalies of similar significance, one involving lepton flavor violation a somewhat similar phenomena, that could have origins in a single theory.

But, a new experimental results, looking at the decays of positively charged pions to electrons and muons respectively, confirms Standard Model prediction of muon-electron universality to within 0.1%.

The electron to muon decay product ratio from charged pions predicted in the Standard Model is (1.2352 ± 0.0002) × 10−4. The experimentally measured value is (1.2344 ± 0.0023(stat) ± 0.0019(syst)) × 10−4, which is 0.0008 × 10−4 less than the Standard Model prediction.  The combined uncertainty of the comparison of the measurement to the prediction (theoretical, statistical and systemic) is about 0.0030 × 10−4. Thus, the difference between the measured result and the predicted one is within a quarter of a standard deviation of the theoretical prediction (suggesting that the true systemic error in the experiment is probably much smaller than reported and is actually nearly zero).

This result makes it appear more likely that the apparent deviations from lepton universality seen at the LHC are actually just statistical flukes or the product of systemic error, rather than actual evidence of beyond the Standard Model physics.

The new result also makes a common source for three modest anomalies seem less likely.

NEMO-3 Set Bounds On Neutrinoless Double Beta Decay

The Standard Model predicts that neutrinoless double beta decay does not occur, because it involves lepton number violation, but many beyond the Standard Model theories, including those in which neutrinos have Majorana mass, predict that neutrinoless double beta decay occurs but it merely very rare, which the frequency being a function of the Majorana mass of the neutrino.

The NEMO-3 experiment using a sample of the isotype Molybdenum-100 sees no instances of neutrinoless double beta decay and sets a minimum half-life on the process of 1.1*1024 years at a 90% confidence interval.

This does not exceed the limits set at GERDA of 2.1*1025 years, in the summer of 2014, which is about 20 times longer, and the most strict limits to date. The next phase of the GERDA experiment will increase its sensitivity by a factor of ten.

The universe is roughly 1.4*109 years old, so the current limit from GERDA means that no more than one in 1.5*1016 of hadrons that could experience neutrinoless double beta decay since the formation of the universe have actually done so.

But, each neutrinoless double decay experiment's null results makes the null result more robust (i.e. not subject to the peculiar methodology issues in any particular experiment) and incrementally increases the combined limit since multiple experiments which all fail to detect neutrinoless double beta decay can all be combined to show the total time that observations have been conducted without seeing the phenomena.

Neutrinoless double beta decay also constrains the maximum Majorana mass of the neutrino.  The limit of less than 0.62 eV set by the NEMO-3 experiment, which is not as strict as those set by cosmology measurements or other neutrinoless beta decay experiments like GERDA, but still forecloses a great deal of parameter space for beyond the Standard Model theories that permit limited lepton number violation.

Thursday, June 18, 2015

Ancient DNA From Kennewick Man Confirms Native American Founder Population Membership

A new study by Rasmussen, et al., entitled "The ancestry and affiliations of Kennewick Man", in the journal Nature was published online today (open access).  Much of the information in the study was available in advance of publication, six months ago.

It finds that ancient DNA from Kennewick Man confirms his membership in the founding population of Native Americans (as opposed to Arctic or Na-Dene populations of Native Americans), despite physical anthropology measurements suggesting an East Eurasian or Polynesian ancestry.  The abstract is as follows:
Kennewick Man, referred to as the Ancient One by Native Americans, is a male human skeleton discovered in Washington state (USA) in 1996 and initially radiocarbon-dated to 8,340–9,200 calibrated years before present (BP). His population affinities have been the subject of scientific debate and legal controversy. 
Based on an initial study of cranial morphology it was asserted that Kennewick Man was neither Native American nor closely related to the claimant Plateau tribes of the Pacific Northwest, who claimed ancestral relationship and requested repatriation under the Native American Graves Protection and Repatriation Act (NAGPRA). The morphological analysis was important to judicial decisions that Kennewick Man was not Native American and that therefore NAGPRA did not apply. Instead of repatriation, additional studies of the remains were permitted. Subsequent craniometric analysis affirmed Kennewick Man to be more closely related to circumpacific groups such as the Ainu and Polynesians than he is to modern Native Americans. 
In order to resolve Kennewick Man’s ancestry and affiliations, we have sequenced his genome to ~1× coverage and compared it to worldwide genomic data including the Ainu and Polynesians. We find that Kennewick Man is closer to modern Native Americans than to any other population worldwide. 
Among the Native American groups for whom genome-wide data are available for comparison, several seem to be descended from a population closely related to that of Kennewick Man, including the Confederated Tribes of the Colville Reservation (Colville), one of the five tribes claiming Kennewick Man. 
We revisit the cranial analyses and find that, as opposed to genomic-wide comparisons, it is not possible on that basis to affiliate Kennewick Man to specific contemporary groups. We therefore conclude based on genetic comparisons that Kennewick Man shows continuity with Native North Americans over at least the last eight millennia.
In short, Kennewick Man's ancient DNA largely confirms the dominant paradigm of the initial human settlement of the Americas, as have other ancient DNA samples from the Americas.

This said, many Native American populations have diverged genetically over time from Kennewick man who is closest to the non-Na-Dene modern Native American populations in the general vicinity of the Pacific Northwest.  Native American ancestry components that are only a part of Kennewick man's DNA are dominant components of many modern Native American populations, suggesting scenarios such as a serial founder effect.

Monday, June 15, 2015

Improved Y-DNA Determination of TMRCA Favors Steppe Hypothesis

It is widely known that estimates of The Most Recent Common Ancestor (TMCRA) of a group of Y-DNA lineages by conventional means grossly overestimates dates that make sense based upon historical and archaeological evidence.

Often the factor that has been used to mitigate the discrepancy has been the implied mutation rate of Y-DNA, but room for manipulation of that calibrating factor has declined as direct measurements of mutation rates have accumulated with a declining margin of error.

But, a preprint by David Hamilton at biorXiv has found another culprit that fits data points from the emerging pool of ancient Y-DNA. The subtle issue is that conventional estimates of TMCRA include only clades that we see, and doesn't make allowance for the fact that many other clades developed in parallel and died off before being observed. Considering this factor generically lowers the TMCRA observed:
Our method for ``Time to most recent common ancestor'' TMRCA of genetic trees for the first time deals with natural selection by apriori mathematics and not as a random factor. Bioprocesses such as ``kin selection'' generate a few overrepresented ``singular lineages'' while almost all other lineages terminate. This non-uniform branching gives greatly exaggerated TMRCA with current methods. Thus we introduce an inhomogenous stochastic process which will detect singular lineages by asymmetries, whose ``reduction'' then gives true TMRCA. Reduction implies younger TMRCA, with smaller errors. This gives a new phylogenetic method for computing mutation rates, with results similar to ``pedigree'' (meiosis) data. Despite these low rates, reduction implies younger TMRCA, with smaller errors. 
We establish accuracy by a comparison across a wide range of time, indeed this is only y-clock giving consistent results for 500-15,000 ybp. In particular we show that the dominant European y-haplotypes R1a1a & R1b1a2, expand from c3700BC, not reaching Anatolia before c3300BC. This contradicts current clocks dating R1b1a2 to either the Neolithic Near East or Paleo-Europe. However our dates match R1a1a & R1b1a2 found in Yamnaya cemetaries of c3300BC . . . together proving R1a1a & R1b1a2 originates in the Russian Steppes.
This methodological advance undermines one of the last genetic evidence arguments for a Neolithic/Anatolian hypothesis of Indo-European linguistic origins in favor of a Copper Age/Bronze Age Steppe hypothesis.

Sunday, June 14, 2015

Pre-History In A Nutshell

Razib has a lengthy synopsis of the recent history of archeogenetics (most of which has happened in my adult lifetime) at Gene Expression to put into context two major new ancient DNA studies in the Journal Nature published this month.

The big headline from these studies is that they provide new ancient DNA confirmation for the increasingly well supported hypothesis that there was an episode of dramatic population genetic change between the first farmer populations of the Neolithic era and modern Europeans, driven by mass migration from the Eurasian steppe, around the time of the early Bronze Age in Europe and almost surely coinciding with a major expansion of the Indo-European languages.

One important emphasis of Razib's account is that the phenotype of the modern European's appearance which we think of when we say that someone is racially "white", like the modern European gene pool more generally, did not really stabilize in Europe until the Bronze Age. Northern Europeans prior to Indo-European migration into Europe, for example, may have been blue eyed but dark skinned, while the invaders from the steppe may have had lighter skin and dark eyes.  The light skinned phenotype we associate with Europeans today didn't reach fixation until the Bronze Age. People who look like typical Northern Europeans today didn't exist when the Egyptians were building their pyramids.

Critics of some of the recent analysis of these studies suggest that important details of the narrative may be inaccurate, because Y-DNA haplogroup subtypes and evidence of ancient Northern European ancestry in some putative parent populations to European populations that were transformed demographically at this time don't track properly to the simplest of narratives advanced to explain the new ancient DNA result.

Wednesday, June 10, 2015

Did The Death Of The Yellow Nile Fragment The Nilo-Saharan Languages?

Wadi Howar - formerly known as the Yellow Nile

Africa has several groups of indigenous languages. In North Africa and East Africa, the Afro-Asiatic languages have been predominant. In West and Central Africa, the Niger-Congo languages are predominant and one subset of those languages, the Bantu languages, are spoken throughout most of sub-Saharan Africa. Hunter-gatherer groups speak a variety of languages with click phonemes that may or may not have a common origin or genetic relationship to each other called the Khoisan languages.

Finally, many nomadic herders of the Sahel and East Africa speak languages that are part of the Nilo-Saharan language family that includes the indigenous languages of several different ethnic groups in Sudan including the people of Darfur, some Nuba Mountain people, the Nubian people, and many of the people of now independent South Sudan.  The people of Darfur, the Nuba Mountain people (both Nilotic speaking and Niger-Congo Kordofani language family speaking) and the Nilotic people of South Sudan have strong genetic similarities with each other (although the ties are far more attenuated in the Nubian people of Northwest Sudan, and the Sudanese ancestral component is somewhat distinct, although still related to other Nilotic populations).

Meinhof in 1911 dubbed the probably Nilo-Saharan languages of Sudan the Eastern Sudanic Languages, also sometimes called the Northern Eastern Sudanic languages (NES).

The history of these languages is intimately connected to the history of one of the greatest rivers that no longer exists, the Yellow Nile, which once rivaled the two main sources of the modern Nile River, the White Nile (which flows more or less due North from Lake Victoria), and the Blue Nile (which flows through Ethiopia to the confluence with White Nile).  As the Yellow Nile (now called Wadi Howar) dried up in the wake of the 4.2 kiloyear climate event and was dealt the final death blow in the climate event that led to the Bronze Age Collapse, the language family spoken up and down the Yellow Nile fragmented into many daughter languages as their civilization collapsed and they were exiled to wander Africa with their herds chasing new sources of water.

A conference paper from 2009 by Dr. Claude Rilly makes the connection.
[W]hen did Proto-NES split into different groups? The earliest attested daughter-language is by far Meroitic. Early scholars thought it appeared in the Nile Valley at the time of the first rulers of Napata, around 850 BCE. However, I have presented elsewhere (Rilly 2007b) evidence that traces of Proto-Meroitic personal names could be found in Egyptian texts dated to the end of the Kingdom of Kerma (ca. 1600 BCE). 
In addition, strong elements in favour of the presence of names fitting with the Proto-Meroitic phonology can be found in the Egyptian lists of bewitched enemies from Kerma as early as the 12th Dynasty (ca. 2000 BCE). Therefore a chronological span around the second half of the third millenium BCE for the splitting of the NES-group is by no means exaggerated. The question is now to find what event caused this splitting.

The University of Cologne have conducted in the last decades an ambitious archaeological project (BOS, later ACACIA, cf. Kuper & Kröpelin 2006, Jesse 2004) in the region of the Wadi Howar. This wadi – also called the "Yellow Nile" – is a former tributary of the Nile running from Ennedi range, in Chad, through Darfur and Kordofan and joining the Nile at el-Debba, north of the great bend of the Nile, 100 km south of Kerma, where the first Kushite state was founded around 2500 BCE. As Eastern Sahara underwent desertification, between 5000 and 3500 BCE, the Wadi Howar attracted a numerous population, especially from the North, until its course became disrupted and finally just temporary around the middle of the 2nd millenium BCE. Nowadays, only the Upper Wadi Howar, in Darfur, retains some water at the time of the seasonal rains. The Wadi Howar was densely populated during three millenia, as can be deduced from the 1700 archaeological sites of various size spotted by the Cologne team. The banks of the wadi are surrounded by additional archaeological sites such as Gebel Tageru in the south, Erg Ennedi in the north and Ennedi range in the west.

Three phases of settlement have been determined in the Wadi Howar. From 5000 to 4000 (phase 1), the river is continuously full and its bank harbour settlements of hunter-gatherers, that live also on fish and molluscs. From 4000 to 2200 (phase 2), the Lower Wadi Howar, close to the Nile, gets dry. New settlers, coming from the neighbouring regions where desertification is gaining ground, are now living mainly on cattle. Goats and sheep are introduced at the end of this period. Contacts with the Nile valley are indicated by imported ceramics of the "herringbone" type. From 2200 to 1100 BCE (phase 3), the whole wadi is dry most of the time, with some humid places during the rainy season in the Upper and Middle Wadi Howar. Settlements are still numerous, but more scattered. The main diet is now made of sheep and goats, as cattle is too exacting for an increasingly arid environment. Donkeys, introduced to Sudan from at least 2500 BCE, play a major role in the nomadic way of life of the last settlers. After 1100 BCE, the region becomes hardly hospitable, excepted in the Upper Wadi Howar.

What can be deduced from the history of Proto-NES fits perfectly with these archaeological and palaeoclimatic data. The crystallisation of the proto-language possibly occurred when cattle-tenders settled together along the Wadi Howar around 4000 BCE, whereas the splitting into different linguistic groups would result from the progressive dessication of the river.
The death of the Yellow Nile coincides closely in time with the death of another famous river, the Saravasti River, which is mentioned frequently in the Hindu epic the Rig Veda, and which archaeological evidence indicates was a lifeline for many of the major cities in the Harappan civilization until it went dry.

META POSTSCRIPT: This is the 800th post at this blog.

Tuesday, June 9, 2015

Bread Came Before Beer; Flour Preceded Domestication Of Grains

A comment by Dorian Fuller to a blog post by Dorian Fuller, the leading archaeobotanist in the world, observes that the archaeological evidence shows that flour and bread making were ubiquitous in the earliest days of the Fertile Crescent Neolithic revolution, while beer appears much later in the archaeological record (disproving a fanciful and somewhat tongue in cheek hypothesis to the contrary).

His main post notes that there was cereal trade in Europe during the Mesolithic era, evidenced by cereals in Southern England, a few thousand years before the Neolithic revolution arrived in England allowing cereals to be grown locally there, and just a few centuries after these cereals were domesticated in the Near East and grown there.

This trade is somewhat less surprising when we note, while we are on the subject of floor and cereals and the sequence in which innovations took place, that flours made from wild grains long predate the domestication of cereals.

Flour is found, for example, in Utah about 10,000 years BP (long before any cereals were domesticated in the New World), and in Tuscany about 25,000 years BP, about 15,000 years before the Neolithic revolution in the Fertile Crescent.
Hunter-gatherers were turning wild plants into flour long before farming was invented.

A find in Utah [citing this source] shows flour being produced 10,000 years ago (long before plants were domesticated in the New World). The "milled seeds include sage, salt bush and various grasses, which were processed on grindstones."

Research at the "Gravettian site of Bilancino, in Tuscany, Italy, which dates to about 25,000 BP uncal [about 28,000 BP on a calibrated basis]. . . . includes notably charcoal, pollen and starch grain recovered from the surface of a grindstone. . . . [T]he occupants of Bilancino had been grinding cattail (Typha latifolia), likely its roots, as well as wild grasses to produce flour."

Why does this matter?
[I]t "implies the availability of an elaborate product, a flour, with high energy content, that is rich in carbohydrates, easily storable and transportable, to make a kind of bread (biscuits) or a porridge" . . . This means that plant material could be preserved and stored for much longer periods of time, which effectively can provide carbs during seasons such as winter during which they are normally difficult if not impossible to obtain. Also, it provides a subsistence items that serves as a buffer against the fluctuating availability of other types of subsitence resources, such as animal tissue. Lastly, because flour is easily ingested and digested, it also provides a foodstuff that both very young and very old members of a group can consume - and maybe even produce while adults are off procuring other things. This means that survival to adulthood and into old age can be facilitated, which has the potential of significantly reorganizing the way labor is divided within a society, and increasing the generational knowledge available to given forager groups.
These finds also further supports the evidence from a variety of sources that modern humans may have had proto-agricultural societies existed for thousands of years before plants were domesticated in a way that made them more useful and permitted a more settled lifestyle with more dense populations.
UPDATE December 13, 2015.  The evidence for Mesolithic cereal trade in Europe turns out to have been flat wrong and the product of inaccurate dating of the evidence.

Monday, June 8, 2015

Why Were The Slavs So Awesome?

A little more than a thousand years ago, not long after the fall of the Western Roman Empire, a group of people from the Balkans Eastern Europe expanded into more or less the entire European region in which Slavic languages are spoken in a migration that had a major demic impact although some pre-existing people were integrated into their society.

Unlike many other known major demic and linguistic expansions, however, the historical forces that allowed the Slavic migrants to utterly swamp the pre-existing residents and bring about language shift are largely unknown and are not even the subject of much speculation, despite the fact that this was happening at the dawn of the historic era and some of the people who witnessed it must have been literate, and despite the fact that the ancestors of these people still live in these places today.

Was there a technology or cultural trait that made this dominance possible?  Had famine or plague or raids by migration era raiding tribes so weakened the existing residents that the land was all but vacant?  If these weren't factors, what were? Investigation of the whys of Slavic migration is a task that should be on the "to do" list of anthropologists and historians as a major unsolved problem.

Wikipedia describes much of what we know about the early Slavs, but this information doesn't itself provide obvious answers to the big question of "why the Slavs were so awesome".

The leading narrative seems to focus on a power vacuum created by the fall of the Roman and Hun Empires, and by the disruption of society caused by raiding tribes (mostly Germanic) in the migration period who raided territory and then left when it was duly pillaged, rather acting like the Slavs and raiding and then ruling the land that they raided.  The Slav had recently rebelled from being overpopulated Iron Age farmers subjugated to barbarians, which presumably made them willing to fight for more land and made them familiar with the raiding lifestyle that they did not fully adopt.

(Factual error corrected later on the same day posted in response to a comment.)

Thursday, June 4, 2015

Koreans With mtDNA C5

In published studies, mtDNA C5 (without further mutations for subclades of C5) is most common among the Paleo-Siberian Ket people near the Yenessi River, makes up about 0.1% of Koreans in published studies of Korean mtDNA, and makes up a bit larger percentage of Mongolians.

But, there are three unrelated individuals with mtDNA C5 and Korean ancestry at 23andMe (in addition to three more individuals, at least, who are related in the maternal line to one of the three).

C5c1 is found in some modern Eastern Europeans with a mutation rate based estimate of its arrival in the Neolithic era, and C5 has been found in Neolithic era mtDNA in Hungary.  But, this derived clade of mtDNA C5 is not found in East Asians.

A Hypothesis Or Two

My working hypothesis is that during the relatively brief period when Korea was under Mongolian rule during the peak of the Mongol Empire in the 13th-14th century, Male Korean aristocrats were frequently required to marry Mongolian princesses by the Mongolian Empire's regime.  The relationships are a plausible source for mtDNA C5 in Koreans, which would otherwise be much more rare.

The Y-DNA impact of Mongol expansion has been explored, for example, here (2003 source article here) but since these events happened in the historic era, we know that Korea was a historically fairly unique case in which introgression of Mongol elites into Korean society was female rather than male biased.

It may be possible to test this hypothesis using genological records.  Korea has one of the longest time series of widespread accurate genological records found anywhere in the world (particularly with elites and the "middle class" such as it was) that goes back about about 750 years to ca. 1250 CE, just long enough to capture the arrival of Mongolian brides.  It would be a painstaking, but relatively straighforward matter to identify individuals with mtDNA C5 and to trace their matriline ancestry back to this time period, although it may very well be the case that North Korean parts of these geneologies may not be available to investigators due to the near total isolation of the current North Korean state.

Another plausible source of mtDNA C5 in Koreans that could explain its rarity in published studies is that it could be more common in North Koreans than in South Koreans, since the vast majority of population genetic evidence about Korea is from North Korea.  At least one of the three 23andMe clusters is specifically North Korean in origin.  North Korea is, of course, geographically closer to the heartland of mtDNA C5 than South Korea, and equally important, more ecologically similar and hence more agreeable for bride exchange and migration based sources.

This could shed light on the existence of ejective glottal consonants in Korean and certain Japonic languages.

Wednesday, June 3, 2015

The Mass Of The Graviton In Massive Gravity Theories

A new pre-print calculates the mass of the graviton in a massive gravity theory consistent with the single parameter that explains galactic rotation curves in MOND theory, the Hubble constant, the proportion of mass-energy in the universe that is dark energy (Omega lambda), the speed of light, and Planck's constant. The formula is h bar/c^2 times the Hubble constant times the square root of three times Omega lambda.

The result is 4*10^-69 kilograms, which is equivalent to 2*10^-33 eV/c^2, which is equivalent to 2*10^-61 times the Planck mass.  The Compton wavelength of a graviton with this mass would be on the order of 100,000 light years (roughly the same as the diameter of the Milky Way galaxy).

Massive gravity theories are candidates for resolving both the dark energy and the dark matter problems of astrophysics.

I am skeptical that gravitons have rest mass.  But, experimental evidence cannot rule out of graviton mass of the scale suggested: the current experimental limit is less than 6*10^-32 eV/c^2 (about thirty times heavier than the predicted value in this preprint).

Gravitons, if they exist at all, however, clearly must have mass-energy, however.  And, massive gravity theory is one way to tease out what general relativity would look like if it treated the mass-energy of gravitons as a source of gravitation curvature (which Einstein's field equations do not).