KhoeSan Genetic Diversity Including Archaic Admixture From A New Archaic Homo Species

Recently analyzed ancient DNA from the greater Middle East has revealed that there were stark genetic differences between populations that where geographically relatively close to each other at the dawn of the Neolithic revolution when the very earliest farming communities had population genetics similar to those of the hunter-gatherers that preceded them - something that would quickly change once the Neolithic revolution really took hold and began a largely demic expansion (i.e. through mass migration rather than cultural diffusion of ideas).

In the Middle East, populations in the Zargos Mountain of Western Iran were as distinct from those in the Levant as Europeans are from East Asians today. In other words, there were distinct racial divisions in the Middle East over distances of just a few hundred miles.

New genetic data from one of the most basal human populations on Earth, the KhoeSan of Southern Africa, suggest that deep genetic divisions between hunter-gatherer populations were the norm, rather than the exception, and have uncovered several new genetically distinct populations ancestral to the KhoeSan which have vanished through full introgression into the South African Bantu and white populations that arrived later.

The study also indicates that in the case of some KhoeSan groups, as has been hinted at in other prior research, that a transition from hunting and gathering to herding can be accomplished with a much larger component of cultural diffusion and a much smaller demic component, than the transition from hunting and gathering to farming.

The name KhoeSan refers to several indigenous populations in southern Africa; KhoeSan people speak "click" languages and include both hunter-gatherer groups and pastoralists. They are genetically distinct and strikingly isolated from all other African populations, suggesting they were among the first groups to diverge from the ancestors of all humans. . . . It quickly became apparent that the geography of the Kalahari Desert was closely tied to the population structure that they uncovered. The outer rim of the Kalahari Desert presented a barrier to genetic mixing, while populations that live within the Kalahari basin mixed more freely.

Their findings suggest a more complex history for the KhoeSan populations than originally predicted. Previous work argued for a northern vs. southern divergence pattern among the human groups, but this new work identifies five primary ancestries in the region, which points to a geographically complex set of migration events responsible for the heterogeneity observed in the region. 

Henn points out that there are more KhoeSan populations who were not sampled. Sampling in the area is a significant challenge for a number of reasons, including the complex politics of the region in the post-Apartheid era. Most populations in South Africa and Zimbabwe no longer identify as KhoeSan and have been absorbed into other populations over the past 500 years. Still, their findings add to the body of knowledge surrounding the history of southern African populations -- while also complicating them

. . .

"There is a huge amount of diversity in southern Africa populations. These groups speak differently, look distinct, and have divergent genetic histories. They are not homogenous people, and the historic and prehistoric factors that led to their divergence are still being explored. It's amazing how much work there is to do."

Via at Science Daily.  The abstract and paper citation to this study are as follows (interestingly, the lead author is still a student):

Recent genetic studies have established that the KhoeSan populations of southern Africa are distinct from all other African populations and have remained largely isolated during human prehistory until ∼2000 years ago. Dozens of different KhoeSan groups exist, belonging to three different language families, but very little is known about their population history. 

We examine new genome-wide polymorphism data and whole mitochondrial genomes for >100 South Africans from the ≠Khomani San and Nama populations of the Northern Cape, analyzed in conjunction with 19 additional southern African populations. 

Our analyses reveal fine-scale population structure in and around the Kalahari Desert. Surprisingly, this structure does not always correspond to linguistic or subsistence categories as previously suggested, but rather reflects the role of geographic barriers and the ecology of the greater Kalahari Basin. Regardless of subsistence strategy, the indigenous Khoe-speaking Nama pastoralists and the N|u-speaking ≠Khomani (formerly hunter-gatherers) share ancestry with other Khoe-speaking forager populations that form a rim around the Kalahari Desert. 

We reconstruct earlier migration patterns and estimate that the southern Kalahari populations were among the last to experience gene flow from Bantu speakers, ∼14 generations ago. We conclude that local adoption of pastoralism, at least by the Nama, appears to have been primarily a cultural process with limited genetic impact from eastern Africa.

C. Uren, et al., "Fine-Scale Human Population Structure in Southern Africa Reflects Ecogeographic Boundaries." Genetics, 2016; 204 (1): 303.

Maju has commentary on the study here.  I've lifted the figure below from the paper from his blog post about it:

Another gem of new genetic information comes from the ASHG 2016 (American Society for Human Genetics) Conference abstracts.  One of those abstracts finds evidence of archaic admixture into the San People from an archaic hominin other than Neanderthals and Denisovans, but more closely related to both than to modern humans.

The sequencing of complete Neanderthal and Denisovan genomes has provided several insights into human history. One important insight stems from the observation that modern non-Africans and archaic populations share more derived alleles than they should if there was no admixture between them. We now know that the ancestors of modern non-Africans met, and introgressed with, Neanderthals and Denisovans. 

The estimate of the quantity of shared derived alleles, the mixture proportion, rests on an assumption of no archaic admixture in African populations, and so African populations have been used as the “non-admixed” outgroup in prior analyses. We find that the story is likely more complex, that the history within Africa involves admixture with population(s) related to Neanderthal and Denisova, and that the mixture proportion estimates for non-African populations have been biased, particularly in Melanesia. 

Here, we present results from a composite likelihood estimator of archaic admixture, which allows multiple sources of archaic admixture. We apply the method to archaic introgression, but it can be used to estimate ancient admixture among any four populations where the modeled assumptions are met. This joint estimate of Neanderthal and Denisovan admixture avoids the biases of previous estimators in populations with admixture from both Neanderthal and Denisova. To correct for dependence in our data, we use a moving blocks bootstrap to calculate confidence intervals. 

With assumptions about population size and more recent population separation dates taken from the literature, we estimate the archaic-modern separation date at ~440,000 ± 300 years ago for all modern human populations. We also estimate the archaic-modern mixture proportion in the 1000 genomes, and the modern genomes sequenced with the high coverage Neanderthal and Denisovan genomes. We report those estimates here, support several prior findings, and provide evidence for a lower level of Denisovan admixture (0.0191 [0.0184, 0.0197]), relative to Neanderthal (0.0256 [0.0247, 0.0265]), in Melanesia. On the basis of an excess of shared derived alleles between San, Neanderthal, and Denisova we suggest that a third archaic population related more closely to Neanderthal and Denisova than to modern humans introgressed into the San genomes studied here.

R. Bohlender, et al., A complex history of archaic admixture in modern humans. (2016).

Prior studies have also found evidence of a couple of archaic admixture into African modern human populations based upon genetic evidence, although no one has been able to recover ancient DNA from any African archaic hominins, mostly due to a lack of conditions suitable to preserve that DNA. This abstract tends to confirm that indeed there was archaic admixture in Africa as well as Eurasia, although again, the particular archaic homo species involved is unknown.

Taming Quantum Gravity

An Approach To Taming Quantum Gravity

Quantum gravity is a Holy Grail of fundamental physics that has eluded physicists for a century. This post considers a theoretical program that could make progress towards this problem by sacrificing theoretical purity in favor of results that produce useful actual calculations.

So far as I know, this strategy has not been heavily utilized by investigators in the fields of gravity and quantum mechanics, even though some interesting results have been generated in this fashion and even though similar approaches are used in QCD.  It is not even generally recognized as a distinct subfield in gravitational physics or quantum mechanics research.

I write this from a big picture perspective (one that professional researchers often lack the luxury to indulge in), fully aware that I am not competent to do much of the work suggested in this research program, and with no idea what this work would actually reveal if it was done. I'm not claiming to have solved the problem of quantum gravity that many greater minds that I have failed to master. Instead, I am suggesting a research program that is more humble in its ambitions than most of the research programs in quantum gravity currently producing publications, in the hope that investigators who are not once in a century geniuses might make useful progress with it by curbing their immediate ambitions and aspirations for their work

The Status Quo

For beginners, I provide some necessary background about the problem of quantum gravity in the context of fundamental physics and about the difficulties that have arisen in formulating a theory of quantum gravity below the fold.

The bottom line conclusion of that analysis is that the principle practical barrier to formulating a theory of quantum gravity based upon the quantum mechanics of a massless spin-2 graviton that has couplings to all fundamental particles proportional to their mass-energy is it cannot be renormalized, which means that you can't make any quantum mechanical calculations with a theory of this kind.

Is Modeling Quantum Gravity Really An Insurmountable Problem?

This seems crazy.

We know for a fact that Nature's true theory of quantum gravity doesn't actually create infinities (at least outside the singularities implied by general relativity and probably not even in all of those cases).

We know for a fact that outside some very highly specific circumstances, it is possible to use very simple calculations (typically using Newtonian gravity as a first order effect and a general relativistic correction, or by truncating classical general relativity in a manner that involves just one or two aspects of it with simplifying assumptions) to make extremely precise predications about all manner of gravitational phenomena.  People were making predictions with general relativity that have been confirmed by 2016 grade instrumentation back in the days when calculations were being done with slide rules and punch card computers.  We sent men to the moon and unmanned spacecraft to the limits to the solar system on exceedingly precise courses using gravitational calculations made with such meager computational power.

A Truncated Quantum Gravity Model Approach

How can this be overcome?

So, even if we are theoretically correct in assuming that Nature's gravity is governed by the quantum mechanics that flow automatically, naturally and elegantly from a massless spin-2 graviton that has couplings to all fundamental particles proportional to their mass-energy including their dynamical energy and preserving all vector components of that motion, from a practical perspective of developing a useable theory of quantum gravity, we are clearly doing it wrong.

There are a couple of instances, mostly in black hole physics, such as the physics of Hawking radiation from black holes, where we take some properties that we expect gravitons to have on an ad hoc basis to reach conclusions with an incomplete quantum gravity theory, but for the most part, we have not embarked on a comprehensive strategy of using incomplete or truncated aspects of a true quantum gravity to get something that is scientifically useful.

One plausible approach, which I can't recall seeing in any published papers or pre-prints is to follow the example of QCD and do calculations for practical purposes not using the complete version of the equations that we believe to describe Nature, but instead, by using an incomplete toy model version of the true equations and then developing a method to assess how much imprecision and inaccuracy is introduced into the result by doing so.

A Quantum Newtonian Gravity Toy Model

As a first iteration of this process, one could formulate a quantum gravity theory that has as its classical limit, Newtonian gravity, rather than general relativity. This can be done with a spin-0 graviton that creates a scalar field. It wouldn't be a perfect approximation, because Newtonian gravity propagates instantaneously while its quantum gravitational version would propagate only at the speed of light.  But, this "error" is actually a good thing, because in general relativity, which better reflects Nature than Newtonian gravity, gravity also propagates at the speed of light.

Using a Newtonian approximation of gravity is justified in a wide range of applications and is routinely done in circumstances where the relativistic modification of the Newtonian result is small because Newtonian gravity is much easier to calculate with than general relativity. Newtonian gravity, for example, is perfectly adequate for even quite sophisticated Earth based applications (e.g. locating underground water and oil reservoirs based upon slight differences in the pull of gravity above them because these liquids have less mass than the solid rock that is elsewhere).  Newtonian gravity also provides an excellent approximation of general relativity in many body calculations in astronomy from the dynamics of planets in the solar system to the dynamics of bodies in asteroids to the dynamics of large many body systems like galaxies.

The Newtonian approximation isn't perfect of course. Using general relativity slightly tweaks the perihelion of Mercury, it gives rise to frame dragging effects in the vicinity of rotating Earth which are just at the limits of state of the art instrumentation to measure, it gives rise to subtle gravito-magnetic effects caused by fast moving heavy objects, it gives rise to gravitational lensing, its cosmological constant gives rise to "dark energy" effects that accelerate the expansion of the universe, it gives rise to gravitational red shifts of photons, it is necessary to model the early universe around the time of the Big Bang, to model the behavior of black holes, and to evaluate pretty much any system with very strong gravitational fields like neutron stars.

Most importantly, there is no good reason to think that quantum gravity is really relevant in any circumstance where even general relativity can be ignored, so in almost every application where Newtonian gravity is an adequate approximation, classical Newtonian gravity is a more practical solution.

But, on the other hand, a quantum gravity version of Newtonian gravity is easy to formulate and to calculate with and can be integrated seamlessly with the rest of the Standard Model.  Also, by estimating theoretical error from the truncation of the infinite series in quantum Newtonian gravity and then adding in the imprecision arising from comparing classical Newtonian gravity to general relativity in any given situation, we can make a very credible estimate of how much precision we are sacrificing when we use quantum Newtonian gravity relative to Nature.

Truncated Quantum Gravity Models Beyond Quantum Newtonian Gravity

A second iteration of this process illustrates why we might want to bother with this approach.

You see, our toy model doesn't have to have as its goal mere replication of Newtonian classical gravity and indeed as we've already seen, even quantum Newtonian gravity automatically fixes one of its flaws by making it propagate at the speed of light rather than instantaneously.

It isn't hard to tweak our quantum Newtonian gravity model to incorporate more features of general relativity (although not all of them) in a manner that can still be renormalized.

For example, it is elementary (and indeed, more natural) to allow our spin-0 graviton to couple not only to particles based upon their rest mass, but also to the energy of photons and gluons in proportion to the energy of these particles and without regard to their direction of motion, which would restore most gravitational lensing (but not necessarily gravitational red shifting) to our model.

We can, and cosmology theorists routinely do, model the cosmological constant of general relativity as a separate quantum mechanical scalar field called "dark energy", rather than as a part of the equations of gravity itself in general relativity.

One of the aspects of the graviton, shared with the gluon, that makes it so much harder to model than photons, is the fact that gravitons couple to gravitons just as gluons couple to gluons, while photons do not couple to other photons since photons lack electromagnetic charge. But, it would be interesting to see what a toy model spin-0 graviton similar to the quantum Newtonian gravity graviton except that it could couple to photons, gluons, spin-0 gravitons and dark energy bosons, would behave like.

I strongly suspect that it would be possible, either by adding in additional kinds of gravitons, perhaps with spin-1, or by tweaking the properties of our spin-0 graviton, to add in further relativistic corrections to quantum Newtonian gravity.

For example, in addition to the dark energy bosons, one could image a model in which one kind of graviton captures most of the gravitational effects of the linear momentum components of the stress-energy tensor to general relativistic gravity, another kind of graviton captures most of the gravitational effects of the angular momentum components of the stress-energy tensor to general relativistic gravity, a third kind of graviton captures directional field flux components of the stress-energy tensor to general relativistic gravity, and our quantum Newtonian gravity spin-0 boson captures the contributions of the rest mass component of the stress-energy tensor to general relativistic gravity.

Perhaps, to simplify the mathematics, the gravitons making vector contributions (i.e. linear momentum, angular momentum and flux) would be modeled as not having interactions with other gravitons, while the spin-0 graviton could be modeled as either interacting with itself, or even interacting with itself and with the other three gravitons making vector contributions to general relativistic gravity.

Admittedly, this approach would be inelegant and would still not capture the cross-interactions of components of the stress-energy tensor with each other and would probably even sacrifice some of the "sacred" foundational axioms of general relativity, for example, by somehow perhaps subtly introducing some kind of frame dependence.

But, it seems to me possible that one could capture not only the first order gravitational effects of general relativity that are reflected in a quantum Newtonian gravity toy model, but also a significant share of the post-Newtonian general relativistic effects of general relativity in such a model without sacrificing the practical necessity of a renormalizable field with which you can do calculations.

And, after all, even in classical general relativity, physicists almost never do analytical calculations using the full complexity of the theory.  Instead, the most widely used calculations truncate full general relativity by using symmetry and other non-physical assumptions and choices of inertial frames in which to do calculations that make the math of one particular aspect of general relativity tractable.

One could also develop means to accurately estimate the magnitude of aspects of general relativity that are ignored by this toy model.  This could be done by direct comparison with classical general relativity in either the toy model calculations actually being done, by direct comparison of the toy model with classical general relativity in the case of a simplified example likely to have comparable general relativistic effects, or most ambitiously by creating analytical expressions of the components of general relativity that are omitted from the quantum gravity toy model (which could be evaluating numerically even if they weren't possible to solve analytically).

What Could Be Achieved With Truncated Quantum Gravity Models?

Suppose then, that we do develop truncated quantum gravity models that deliberately omit the aspects of general relativity that make it impossible to renormalize, while estimating the magnitude of the effects of the omissions in some credible way.

The hope would be that these models could be used to create a workable substitute for Nature's quantum gravity, that is amenable to numerical calculation, whose phenomenology could be used to understand how true quantum gravity would behave in a significant class of circumstances in which (1) it is plausible that there are measurable quantum gravity effects, and (2) we can determine that the magnitude of the general relativistic effects omitted in the truncation are much smaller than the magnitude of the measurable quantum gravity effects in the truncation.

For example, I suspect that such a model could work quite well to evaluate the phenomenology that a true quantum gravity theory would have in weak gravitational fields relative to general relativity, which would have potentially widespread practical relevance in particle physics and astronomy. For example, very heavy exotic matter created in particle accelerators might create weak gravitational fields that are not so weak that they can be entirely ignored in precision calculations. And, these models could be used to create middle ground between using pure Newtonian gravity in many body galaxy and cosmology models and using full fledged classical general relativity which is often mathematically intractable.

Indeed, it might be possible, by using a variety of different truncations, to credibly measure the magnitude and nature of multiple quantum gravity effects (even in the same hypothetical physical system), even though it would be impossible to renormalize a quantum gravity model that included all of these general relativistic effects at the same time.

Most idealistically of all, one might hope that by making piecemeal progress in understanding what quantum gravity does and does not do in particular applied circumstances, that the scientific community could develop well founded expectations about quantum gravity phenomenology, and insights into the nature of the quantum mechanical calculations which could shed light on terms in the fully quantum gravity of Nature that are and are not important, that might lead to insights that make it possible to do full fledged quantum gravity of Nature calculations, for example, by developing good intuitions about how to cause immaterial terms in the full quantum gravity calculations to cancel out or to be segregated from important terms, in order to make full quantum gravity mathematically tractable.

More Ancient Jomon DNA

A new analysis of two autosomal DNA samples from 3000 years old Jomon (indigenous Japanese) individuals has been released.  This timing would be immediately before or at the time of first sustained contact with the mainland rice farming Yaoyi whose admixture with the Jomon grave rise to most of the modern Japanese gene pool.

Methodologically, this study is distinct because it pools the two ancient DNA samples into one composite sample for analysis of relatedness to other populations since the coverage for each of the individuals separately was poor. The discussion of efforts made to determine the validity of this approach in the paper convincingly demonstrate that this is proper for ancestry analysis purposes.

Like previous studies, it shows a greater Jomon affinity to the Japanese, and in particular to the Ainu and Ryukyuan populations than any other.  Likewise, it shows Ainu admixture with Siberian populations that is absent in all ancient Jomon DNA samples and in the Japanese populations that have Jomon admixture from further south than the territory inhabited by the Ainu.

But, the study's estimate of the autosomal contribution of the Jomon to the modern mainland Japanese (12%) is on the low end compared to both prior studies (18%-35%) and the frequency of Y-DNA (35%-45%) and mtDNA (about 35%) traces of the Jomon in modern Japanese populations.  It isn't obvious why this would be the case. Perhaps bias due to incomplete sample quality that prevents matches to Japanese DNA that would have been possible to make in better preserved samples could be a factor.

The study also suggests that the Jomon have a West Eurasian leaning genetically, relative to modern Asian populations and that this population, as expected, is basal relative to modern Asian populations other than Papuans.

A new top quark mass measurement from CMS

A first measurement is presented of the top quark mass using the decay channel t to (W to l nu) (b to J/psi+X to mu+mu- + X), in events selected in proton-proton collisions and recorded with the CMS detector at the LHC at a center-of-mass energy of 8TeV. The data correspond to an integrated luminosity of 19.7 inverse femtobarns, with 666 ttbar and single top quark candidate events containing a reconstructed J/psi candidate decaying into an oppositely-charged muon pair. The mass of the (J/psi+l) system, where l is an electron or a muon from W boson decay, is used to extract a top quark mass of 173.5 +/- 3.0 (stat) +/- 0.9 (syst) GeV

CMS Collaboration, "Measurement of the mass of the top quark in decays with a J/psi meson in pp collisions at 8 TeV" (August 11, 2016).

A combined margin of error of about +/- 3.13 GeV makes the new result almost useless, however, and even in a combined measurement, it would be weighted very minimally as a result of the lack of precision.

Still, the fact that the central result is quote close to the global average in a decay path not previously measured, does help make the existing estimate more robust and supports the integrity of the Standard Model in which the mass is calculated.

Prestige Necropolis In North America Better Understood

In Egypt, the pyramids were the ultimate prestige grave sites that shed light on their ancient civilization. Mound 72, discovered by archaeologists in 1967, is what appears to be Cahokia's greatest prestige necropolis.

Cahokia, in modern day Saint Louis, was the capitol of a great copper age, pre-Columbian maize and pumpkin farming civilization of North America which flourished around 1,000 CE. This civilization extended to more or less the entire Mississippi basin and has trade links and cultural influence, at least, that extended as far as the Carolina coast. At its peak, about 75,000 people lived in the capitol, making in a world class city by pre-Bronze Age standards.

Predecessors of the Cahokia civilization may have even been a cultural source for the Mayans, as its predecessor civilizations in Louisiana produced the earliest discovered pyramids in the Americas.

Until now, Mound 72 was believed to have six bodies, all men, presumably kings or heroes. But, further research has determined that there are at least twelve bodies there, including many male-female couples.

This tends to show that there may have been an aristocracy in this civilization in which aristocratic men and women played important roles, until male warrior dominated societies arose in the vicinity of this empire after its collapse. Cahokia's decline began around the 1160s and 1170s during a major New World drought, and eventually collapsed as an urban complex around 1350 CE around the time of the Little Ice Age. The last vestigial remnants of this culture were wiped out when European diseases struck relict communities shortly after Columbus and the conquistadors who followed him made contact with the New World.

The abstract and citation of the source paper are as follows:

The Beaded Burial central to F101 within Cahokia's mound 72Sub1 has been fundamental to some cosmological explanations of the founding of this North American precolumbian polity. The central burial, identified as two males surrounded by retainers, has been interpreted as paradigmatic of a paramount chiefdom, or conversely, as a mythic cosmogram. Recent bioarchaeological reanalysis and two independent osteological studies of F101 and associated burials have identified the presence of male/female pairs, numerous females, and at least one child, suggesting that previous explanations privileging the male Red Horn association should be reexamined. We suggest that 72Sub1 is most likely correlated with ritual practices promoting world creation, renewal, and fertility symbolism.

Thomas E. Emerson, et al., "Paradigms Lost: Reconfiguring Cahokia's Mound 72 Beaded Burial." 81(3) American Antiquity 405 (2016).

Chinese Legendary History Coroborated

China’s historiographical traditions tell of the successful control of a Great Flood leading to the establishment of the Xia dynasty and the beginning of civilization. However, the historicity of the flood and Xia remain controversial. Here, we reconstruct an earthquake-induced landslide dam outburst flood on the Yellow River about 1920 BCE that ranks as one of the largest freshwater floods of the Holocene and could account for the Great Flood. This would place the beginning of Xia at ~1900 BCE, several centuries later than traditionally thought. This date coincides with the major transition from the Neolithic to Bronze Age in the Yellow River valley and supports hypotheses that the primary state-level society of the Erlitou culture is an archaeological manifestation of the Xia dynasty.

Qinglong Wu, "Outburst flood at 1920 BCE supports historicity of China’s Great Flood and the Xia dynasty" Science (05 Aug 2016) Vol. 353, Issue 6299, pp. 579-582 via Dienekes' Anthropology Blog.

Lubos Motl on New Experimental Physics Results

All babies are being killed and embryos are being aborted these days.

- The Reference Frame.

In other words, beyond the Standard Model physics proposals are being ruled out left and right.

Sabine Hossenfelder at Backreaction likewise bemoans the arrival of the "Nightmare Scenario" in which the LHC is discovering no new physics other than the Higgs boson.  She thinks that there's a moral to the story:

That the LHC hasn’t seen evidence for new physics is to me a clear signal that we’ve been doing something wrong, that our experience from constructing the standard model is no longer a promising direction to continue. We’ve maneuvered ourselves into a dead end by relying on aesthetic guidance to decide which experiments are the most promising. I hope that this latest null result will send a clear message that you can’t trust the judgement of scientists whose future funding depends on their continued optimism.

I agree that particle physics has put too many of its eggs in the same SUSY/string theory basket, and even more on theories that have the same philosophical motivation.

750 GeV Resonance Gone, SM Repeatedly Confirmed, Higgs Boson Trending Lighter

Lubos Motl has a good summary of the CMS experiment's results based upon the first day of talks at the ICHEP conference in Chicago and some related papers that were released.

Jester's twitter feed provides some charts and analysis generally confirming his conclusions.  So does Matt Strassler's blog.

1. There Is No 750 GeV Bump. The big news is the highly anticipated (and widely rumored) result related to the 750 GeV diphoton bump. A prematurely released CMS paper on the 750 GeV resonance, a bump that has spawned 500 recent papers over roughly the last half year, shows that it has disappeared with the new data. How much new data? Much more than the data set that provide the initial evidence of a bump.

The relevant portion of the data taken by CMS in 2016 is usually given by 12.9 inverse femtobarns of data. Note that this whole 12.9 was taken in the first half of 2016. They never combine the 2015 and 2016 data. They could combine them and increase 12.9 by something like 2.7 that is used in many CMS papers based on the 2015 data.

UPDATE: ATLAS concurs that the 750 GeV bump is not present in the new data (full paper here). See also here.

2. Standard Model Confirmation. The overwhelming share of 39 papers dumped by CMS in connection with the conference perfectly confirm the Standard Model in all but 7 cases (with multiple hypotheses tested in each of most of the papers).  Only one result had a deviation from the Standard Model with more than 2.6 sigma of statistical significance, and that has a 2.84 sigma global significance.  This is in the ballpark for the number of anomalies of this significance that would be expected due to random statistical flukes in a dump of this many results at once.

Only a couple of the anomalies also showed up in previous data sets and at least one of those had an anomaly of declining statistical significance despite the fact that a larger data set that should increase the statistical significance of an anomaly found in prior data that was real by about 2.5 sigma over the previous data set.  So far, there is also no meaningful ATLAS confirmation of the CMS anomalies.

SUSY exclusions and other BSM exclusions exclude more parameter space than they did after the last round of data was analyzed.  Some SUSY exclusions rule out certain sparticals (gluinos) under certain assumptions up to 1.9 TeV.

3. Higgs Boson Mass.  The latest measurement of the Higgs boson mass (based upon four lepton events) by CMS was 124.5 +0.48/-0.46 GeV. This is less than the current global average of about 125.09 +/- 0.24 GeV, which is statistically consistent with the global average but will probably drag down a new global average somewhat, although there is a considerable range of data points that contribute to that global average.

What does the new CMS Higgs boson measurement mean in context?

The current combined estimate of the Higgs boson mass (from the link to that value above) is based upon the following data points:

* ATLAS diphoton mass 126.02 +/- 0.51 GeV
* ATLAS four lepton mass 124.51 +/- 0.52 GeV
* CMS diphoton mass 124.7 +/- 0.34 GeV
* CMS four lepton mass 125.59 +/- 0.45 GeV

So, after this new CMS data point, the new global average should be roughly 124.82 GeV with a pretty similar margin of error, before accounting for any new ATLAS results with its wealth of new data.

The new CMS data point also makes the ATLAS diphoton data point look like an outlier relative to the other three measurements, which suggests that we may expect the combined average is more likely to fall than to rise when ATLAS releases its next Higgs boson diphoton decay based mass measurement, bringing the combined average closer to the theoretically notable value of 124.65 GeV discussed below.

Some of the prior Higgs boson mass measurements at the LHC (by date of publication, some of which were used in the current combined average) include the following:

* ATLAS diphoton mass 125.98 +/- 0.42 +/- 0.28 (June 15, 2014)
* ATLAS four lepton mass 124.51 +0.52 +/- 0.06 (June 15, 2014)
* CMS diphoton number 124.7 +/- 0.31 +/- 0.15 (July 2, 2014)
* CMS four lepton mass 125.6 +/- 0.4 +/- 0.2 (September 10, 2014)

The new CMS four lepton mass measurement is very close to the June 15, 2014 ATLAS four lepton mass measurement.

The downward trend in the Higgs boson mass revives the possibility that the sum of the squares of the fundamental boson masses is equal to half of the square of the Higgs vacuum expectation value (VEV).  The Higgs boson mass in that scenario would be 124.65 GeV (which is robust to variations within the current margin of error of the W and Z boson masses).  This is consistent within two sigma of the current global average, within one sigma of the latest CMS four lepton based measurement of the Higgs boson mass, and even closer to the likely combined global average once the new CMS result is considered.

It also further disfavors the 2W+Z=2H mass formula, which is already disfavored by 3.7 sigma with the current global average, to the point that it is pretty much conclusively ruled out.

As previously noted at this blog:

There is an argument that the "tree-level" mass of the Higgs boson is 123.114 GeV (half the Higgs vev) but that it is increased by higher order loop corrections that bring it to its experimental value. The "tree-level" estimate of the mass of the W boson is 78.9 GeV. If the percentage increase in mass due to higher order loop corrections for the Higgs boson from the tree level value is the same as the higher order loop corrections of the W boson to the experimental value, then the implied Higgs boson mass value would be 125.43 GeV which is consistent at a 1.4 sigma level with the latest combined mass measurement. No published source actually calculates these higher order loop adjustments, however. While the actual higher order loop calculation is probably of that order of magnitude, it could easily be higher or lower. The claim is plausible, but requires further investigation. If the higher order loop corrections produced a value consistent with 124.65 GeV, that would be remarkable indeed[.] . . . 

This also significantly tightens the expected value of the top mass from the formula that the sum of the square of each of the fundamental particle masses equals the square of the Higgs vacuum expectation value. The uncertainty in the Higgs boson mass had been the second greatest source of uncertainty in that calculation. The best fit for the top quark mass on that basis (using a global fit value of 80.376 GeV for the W boson rather than the PDG value) is 173.73 GeV (173.39 to 174.07 GeV within the plus or minus one sigma band of the current Higgs boson measurement). 

If the the sum of the square of the boson masses equals the sum of the square of the fermion masses the implied top quark mass is 174.03 GeV if pole masses of the quarks are used, and 174.05 GeV if MS masses at typical scales are used.

That compares to the latest top quark mass estimate from ATLAS of 172.99 +/- 0.91 GeV. The latest combined mass estimate of the top quark (excluding the latest top quark mass measurement estimate from ATLAS) is 173.34 +/- 0.76 GeV.

The expected value of the top mass from the formula that the sum of the square of each of the fundamental particle masses equals the square of the Higgs vacuum expectation value, goes up if the Higgs boson mass is reduced.

Other Higgs boson news:

In general, there have been a long string of Higgs boson reports from the LHC tending to show a very tight correspondence between all of the experimentally measured properties of the Higgs boson and the theoretically predicted properties of a Higgs boson of roughly the measured Higgs boson mass. The latest measurements of Higgs boson properties announced today are no exception to this trend.

Strong (3.3 sigma) but not discovery level evidence is found at ATLAS for a Higgs process involving top quark pairs in the frequencies consistent with those predicted by the Standard Model.

Previous experiments have also confirmed that the Higgs boson is spin-0, even parity, and has couplings of the predicted strength all of the now nearly half dozen couplings that have been measured.

Back To Basics About Supersymmetry

The following questions and answers are copied from questions posted and answers I wrote at the Physics Forum (with some significant editing, expanded text, and reformating):

Questions:

What is the point of sparticles? What will they prove? How will they work? I've read about supersymmetry, but don't really get it. I know it is to unify quantum mechanics and relativity, but how?

Answer:

Sparticles are particles beyond the Standard Model of particle physics that are necessary for supersymmetry which is a generalization of the Standard Model of particle physics that is attractive for reasons of interest to theoretical physicists.

Standard Model Fundamental Fermions and Bosons

In the Standard Model of particle physics, there are two basic kinds of particles.

In the Standard Model, fundamental fermions are the building blocks of what we crudely in layman's language think about as "matter".  For example, a hydrogen atom is made of three quarks that combine to form a proton with an electron orbiting around it. The six kinds of quarks are fundamental fermions, and these fundamental fermions combine to make protons, neutrons and more exotic composite particles called hadrons which are made of two (mesons) or three (baryons) or more quarks.  Particles made up of quarks are often accompanied by orbiting electrons, or muons (heavy electrons), or taus (really heavy electrons).  When muons and taus and other fundamental particles decay into lighter particles they spew out one of three kinds of neutrinos (which are very light, but non-zero mass particles that interact barely at all except via the weak force and gravity).  Electrons, muons, taus and the three kinds of neutrinos combined are fundamental fermions that are similar in certain ways and are collectively called leptons. 

In the Standard Model, fundamental bosons are we crudely think of in layman's language as the particles that make up force fields.  Electromagnetic fields are made of bosons called photons. Protons and neutrons and other particles made of quarks (which are fundamental fermions) that are held together by bosons called gluons which carry the strong force.  The weak force is carried by bosons called the W boson (for "weak") and the Z boson (because they needed to give it a name and didn't have any other good ones). Gravity, if it is a field carried by a particle is carried by a hypothetical boson called a graviton.  The Higgs boson carries the "Higgs field" which gives fundamental particles their mass (it isn't clear whether or not the Higgs boson interacts with neutrinos which may get their mass in a different way, how neutrinos get their mass is an unsolved problem in physics).

Supersymmetry Is A Balance Between Fundamental Fermions and Fundamental Bosons

Without getting into all the technical details, supersymmetry (also known as SUSY) is basically about the idea that there are technical reasons that makes it desirable for there to be a fundamental balance between fundamental fermions and fundamental bosons.

The theoretically easiest way to get that balance is to imagine that every fundamental fermion has a new fundamental particle boson counterpart (squarks and sleptons), and that every fundamental boson has a new fundamental fermion counterpart, which have their own special names.* These partner particles are "sparticles."

This then gets jumbled a bit because some of these counterparts have very similar physical properties that cause them to blend into each other and look like different particles (something that happens in the Standard Model as well in the way that the electromagnetic force and weak force are related to each other in very deep ways call electroweak unification), and the theory also requires at least four extra Higgs bosons to work out (a positively charged one, a negatively charged one, an extra heavy one, and one with a different parity - i.e. left handedness v. right handedness than a usual Higgs boson).

More complicated "non-minimal" versions of supersymmetry assume even more new particles.

* It could be that a balance between fundamental fermions and fundamental bosons already exists in the Standard Model in a much more subtle way than the crude and obvious balancing present in supersymmetry theories, which would explain how seemingly "unnatural" aspects of the Standard Model "miraculously" balance out, but so far only the vaguest hints that this might be the case have been worked out by theoretical physicists and only as conjectures and hypotheses, not as proven theories.

Supersymmetry is a GUT and SUGRA is a TOE.

Supersymmetry itself does not unify quantum mechanics and relativity. Instead, it unifies the three forces of the Standard Model (electromagnetism, strong force, weak force) into forms of the same underlying force that is unified at high energies, making it what is known as a Grand Unified Theory (GUT). Supersymmetry also ties in naturally to some mathematical structures known as "groups" in a more elegant way than the Standard Model does (which takes at least three different groups crudely "glued" together to summarize).

If you add quantum gravity to the supersymmetry mix by adding the graviton (a fundamental boson) and a superpartner called a gravitino (a fundamental fermion), you get supergravity also known as SUGRA which is a low energy approximation of a Theory of Everything (TOE), and supergravity, in turn is usually a foundation of string theory.

Why Isn't Supersymmetry Noticeable In Daily Life?

We don't notice any of this in everyday life, or even in high energy physics experiments (if the theory is true) because all of the particles created by supersymmetry except one (which explains dark matter and interacts with other matter no more strongly than neutrinos do) are unstable and decay into ordinary matter before we have time to see it, and also because they only form at all in very high energy situations.

If this sounds familiar, it should. Most of the particles we do know exist decay extremely rapidly into ordinary matter and only form at all in very unusual high energy situations, or are always found confined in composite particles and never seen in isolation, or are neutrinos which are extremely hard to detect because they interact so weakly with everything else.

In daily life, we see mostly protons and neutrons (which are made mostly out of up quarks and down quarks bound together by gluons so tightly that we never see free quarks or free gluons), electrons, and photons.  The force that connections protons and neutrons in the nucleus of an atom is carried mostly by pions which are made up of two up and down quarks bound by gluons which are themselves short lived and travel only short distances before decaying (with the quarks and gluons never visible in isolation).  All other particles in the Standard Model are too ephemeral or ghostlike to notice without high technology instrumentation in carefully constructed lab experiments.  

The vast majority of physics (except radioactivity and high energy physics) can be explained with protons, neutrons, pions, electrons and photons (the first three of which are not actually fundamental), without knowing about the huge menagerie of fundamental particles and composite particles needed to describe the last 0.1% of reality.

Supersymmetry just adds more exotic, ephemeral fundamental particles and particles that are very hard to detect (a dark matter candidate called a WIMP) to the mix for relative obscure theoretical reasons set forth in the next section.

Why Supersymmetry?

Supersymmetry is attractive as a theory for many reasons, some of which are now obsolete:

(1) It provides natural candidates for dark matter particles of a variety called "WIMPS".

(2) It makes the constants of the Standard Model such as the Higgs boson mass seem more "natural".

(3) It makes it much easier to do math that sheds light on how particles interact at very high energy, because the balance between fermions and bosons makes lots of terms in calculations that would otherwise have to be calculated cancel out.

(4) It unified the three fundamental forces into one master force at high energies called the GUT scale.

(5) It provides a way to explain where the matter in the universe came from that are unexplained in the Standard Model.

(6) It sheds some light on the kind of reasons that Standard Model constants might have the values they do although not particular clear guidance.

(7) Supersymmetry is so mathematically similar to the Standard Model of particle physics, it is easy to tweak properties of particular versions of supersymmetry like particle masses in such a way that it predicts essentially the same things as the Standard Model down to the limits of experimental error. So it is hard to reject outright.

(8) Before we knew the mass of the Higgs boson, lots of Standard Model predictions in high energy situations were nonsense answers where the likelihood of all possible events didn't add up to 100% if Higgs boson mass is not just right, but this doesn't happen in supersymmetry.  This is less of a big deal than it used to be because the mass of the recently discovered Higgs boson is "just right" and prevents the Standard Model from becoming pathological mathematically at high energies in the way that it would if the Higgs boson where much heavier or much lighter than it is in reality. 

(9) Supersymmetry is also a very natural low energy approximation of string theory.  Many versions of string theory require, for mathematical reasons, that fundamental fermions and fundamental bosons have counterparts for each other for reasons related to the way a fundamental superstring in that theory can vibrate.

Theoretical physicists are very reluctant to abandon supersymmetry because that would mean giving up hope that their best shot at a good theory of quantum gravity through string theory as explained below. So they'd have to start over from scratch trying to merge quantum mechanics and general relativity. 

Why String Theory?

The Standard Model and general relativity are mathematically incompatible with each other. The reasons that the Standard Model (i.e. quantum mechanics) and general relativity are incompatible are quite mathematical and technical but include, for example, the fact that point particles which are assumed in quantum mechanics would instantly turn into black holes in general relativity.

The Standard Model and supersymmetry are both fully compatible with special relativity, however.

Scientists from Einstein onward have been trying very hard to unify gravity and other forces of nature ever since general relativity and quantum mechanics were conceived in the early 1900s. So far, no one has even come close to succeeding.

A potential connection to string theory is attractive because string theory offers a reasonable hope that it could provide a mathematically consistent way to create a theory of quantum gravity that could be consistent with the rest of quantum mechanics which is called the Standard Model. 

String theory is pretty much the only game in town that creates a potential theory of quantum gravity with particle based force fields like those used in the rest of quantum mechanics so it is very tempting to find a way to connect what we know to it.

There is another approach to quantum gravity that involves applying quantum mechanical concepts to the nature of space-time itself, which includes approaches known as Loop Quantum Gravity (LQG), rather than using the force field carried by particles approach of string theory, but that is a story for another day that doesn't involve supersymmetry.

Why Not Supersymmetry?

The obvious problem with supersymmetry is that nobody has ever seen any of the supersymmetric particles, either because they are not real, or because the new particles are simply too heavy to see in colliders, or because they are otherwise not visible due to something called "R-parity" (a property that basically keeps sparticles and regular matter separated).

(1) If superpartners exist, the LHC has determined that they are much heavier than they were expected to be.  At some point, if they are not found at low enough masses, they would be so heavy that they would lead to predictions that are contrary to experimental evidence.

(2) "Naturalness" which is an important reason for supersymmetry is being questioned as a useful theoretical concept.

(3) The evidence of force unification that should have showed up by now has not appeared.  

(4) And, the LUX experiment has pretty much ruled out the kinds of WIMP dark matter particles that supersymmetry predicted.

Why Not String Theory?

String theory has all of the problems of SUSY and SUGRA and also lots of problems of its own. Basically, there are thousands or millions or more versions of string theory (called "vacua") and nobody knows which version is remotely close to our reality.

Where Does This Leave Us?

The Standard Model, in contrast, has no obvious generalizations that could for example be used as a basis for a version of string theory. So figuring out how to meld it with quantum gravity is even more difficult.

Coming Attractions

The latest results from the LHC on the 750 GeV "bump" in the data is scheduled to be released at a conference which begins on August 3, 2016, a week from yesterday.

This "bump" which now appears to have been nothing more profound than a statistical fluke, spawned intense interest from the theoretical physics community that resulted in publication of more than five hundred journal article pre-prints in the span of just a few months (see also here in a post at this blog of the same name as this one).

The rumor mill has it that the results will not involve a 5 sigma "discovery" threshold finding and will probably show declining statistical significance.  Indeed, the rumor is that the 750 GeV "bump" is basically dead (as I predicted it would be on this blog when the results were first announced). But, of course, we'll have a far more precise answer soon.

The minimal model of the Standard Model together with General Relativity with a cosmological constant continues to reign supreme, explaining pretty much everything except dark matter phenomena.  Light sterile neutrinos are essentially ruled out too.

Add to this the failure of direct detection experiments and of satellites trying to detect dark matter annihilation signatures (and a lot of other data) is putting tight constraints on any particle based dark matter solution and ruling out conventional SUSY WIMPS.  Not all dark matter particles are ruled out yet, however, and no really wholeheartedly convincing true quantum gravity theory to explain dark matter phenomena is in place either, even though some intriguing efforts has been made on that front.

Ashkenazi Jewish Genetics

Most Jews are either Ashkenazi Jews or Sephardic Jews, and most American Jews are Ashkenazi Jews, typically with origins someplace in Eastern Europe immediately prior to immigration to the United States.

A new paper looks at the genomes of Ashkenazi Jews today in order to determine their population history using computerized tools and a greatly expanded set of Jewish and non-Jewish reference genomes that has accumulated over the last few years. 

This is necessary because the historical record provides very little meaningful or reliable insight into the process by which the Jewish diaspora resulted in migrations of Jews from the Middle East to Europe. The gap in the historical record is particularly acute in the several century long gap period after the composition of the Babylonian Talmud and the fall of the Roman Empire, and before the pogroms directed at Jews in Europe which roughly coincided with the Crusades. Yet, this gap period was apparently the period of Ashkenazi Jewish ethnogenesis and the source of the population bottleneck that is a defining feature of Ashkenazi Jewish population genetics.

The quaint term for this time period in historical circles is the "dark ages" and the dearth of historical sources from that era deserve that name, even though we do know a fair amount about that time period now by a variety of means. This time period overlaps with the expansion of the Islamic empire, the Slavic expansion in Eastern Europe, the "migration period" of (mostly) Germanic tribes in Europe, and Anglo-Saxon and Viking raids into and migration of England (which is arguably part of the migration period).

The genetic analysis is not straightforward because (1) there are considerable similarities between the genetic profiles of the suspected source populations, (2) there is little ancient DNA to bear on the question very directly, and (3) modern populations are not great proxies of historical populations at the time that the relevant stages of the migrations happened, particularly in the Levant and Slavic Europe. Indeed, the latest results come with considerable acknowledged uncertainty, although the broad outlines of the analysis are probably correct.

The West Hunter blog has a summary of the findings of this open access paper that fairly states the conclusions of the paper at least as well as I could describe them myself:

When they analyze the origins of the European component of Ashkenazi ancestry, they conclude that most is southern – probably Italian, but that smaller amounts originated from (probably) Western Europe and (more certainly) Eastern Europe: and in that temporal order. They conclude that the Italian admixture slightly predated a late medieval founder event. Different methods came up with somewhat different estimates for the total amount of European ancestry: the local ancestry inference (LAI) approach came up with 53% European, while the GLOBETROTTER analysis came up with an estimate of 67% European ancestry (after calibration by simulations). In their best guess, they split the difference and go for 60% European.

To sum up, their model is that a population from the Levant mixed with Italians, and shortly thereafter moved to the Rhineland (the founding bottleneck), perhaps mixing to some degree with the local Europeans there, and certainly mixing some with Slavic types when they moved to the Polish-Lithuanian Commonwealth.

How do their conclusions differ from those in the last report? Previously they were thinking that the bottleneck was around 1350, a product of the Black Death and savage persecution – now they’re talking the original settlement in the Rhineland. Previously they had a somewhat lower estimate of European ancestry (~48%, now 60%). I thought these two conclusions likely a couple of years ago. 

The big new point, important if correct, is that the admixture with Italians is relatively recent – too recent to have happened back in Roman times. In their model, this main admixture event is 25-55 generations ago, while the founding bottleneck is 25-35 generations ago. It’s not impossible that the admixture happened at the same time as the founding.

About 15%-25% of Ashkenazi Jewish ancestry, which is a quarter to a almost half or so of the total European ancestry, is Eastern European.  I've also seen other sources conclude that the paternal line is more strongly Levantine than Jewish maternal ancestry.

As Razib Khan has noted in comments to his post on the same paper, the Black Plague hypothesis was always suspect as a source of the population bottleneck that is clearly apparent in Ashkenazi Jewish population genetics, because it didn't kill a large enough percentage of the population to be likely to have caused the observed bottleneck effects.

This is also as good a post as any to observe that all Jewish populations in the world from Ashkenazi and Sephardic Jews to Jews in Yemen, India and elsewhere, are significantly admixed with local populations. Endogamy in the founding populations of Jews in the Jewish diaspora has almost always been modest in the founding period, even though these barriers to admixture ossified with time. There are probably far fewer "pure blooded" Jews with exclusively Levantine origins and descended from Jews in their Iron Age kingdoms (I'm not convinced that there are any), than there are "pure blooded" Native Americans who lack European or African admixture, for example.

Lux Further Constrains Dark Matter Parameter Space By A Factor Of Four

Lux is the gold standard for direct dark matter detection experiments and has further ruled out forms of dark matter that slightly interact with ordinary matter to a much greater degree.  Any dark matter particles with masses from 1 GeV to 10,000 GeV that have interactions with ordinary matter that are more than a fraction of the strength of interactions of a neutrino (which is barely any at all) have been ruled out.

The WIMP paradigm (in the narrow sense of dark matter particles that interact via both the weak force and gravity) is well and truly dead.

From Quantum Mechanics To Gravity

Sean Carroll's latest paper considers (but doesn't really prove) a couple of interesting conjectures:

1. Gravity and space-time geometry are emergent properties of a quantum world that reflect the degree to which particles are entangled with each other (more entanglement implies shorter distances and the mass-energy coupling might emerge more or less naturally and automatically from the formulation).

2. Nature is a quantum system in a finite dimensional Hilbert space, rather than an infinite dimensional Hilbert space as generally assume in quantum mechanics, which would provide a natural (but elegant) cutoff that would insulate the real world from the infinities and singularities found in quantum mechanics and GR done in an infinite dimensional/continuous approximation.

More On Madagascar's Genetic Origins

The biggest surprises of a new paper on the genetic origins of the people of Madagascar are the roughly 2/3rds African origin demonstrated when some previous estimates had been closer to 35%-50%, and more surprisingly, that the affinity of that African component to Southern African Bantu, when previous data had rejected that hypothesis in favor of an affinity to East African Bantu populations (less some recent Nilo-Saharan admixture).

Southern African Bantu have a substrate of pre-Bantu Mozambique people which is very distinctive from any extant African population to the extent that it basically constitutes a "lost race" of Africans that coincides with linguistic substrates of Bantu languages in that region indicating that the pre-Bantu people of Mozambique spoke a click language.  There are also uniparental markers private to Mozambique that are largely absent from Madagascar.  So, there are strong reasons to be skeptical of a Southern African as opposed to East African source for the African genetic contribution to Madagascar.

The lack of a strong historical connection between Mozambique across the strait from Madagascar and that island is likewise demonstrated by a lack of archaeological support for those kinds of trade ties and a lack of Southeast Asian genetic traces in mainland Africa (anywhere).

The conclusions on the Asian genetic origins side of the analysis, on the other hand, are plausible and very consistent with previous research on the topic, although the analysis does not identify indications from previous studies that the migration was probably along the Indian Ocean's coast with stops in South Asia and East Africa, rather than directly across the Indian Ocean as a graphic in the new paper misleadingly suggests.

I'll need to look more closely at the various papers involved to see if these new results can be reconciled with the prior research, and if not, to determine the likely source of the disparity.  The two-thirds percentage is probably right, but the South African Bantu affinity seems suspect. The fact that only the Asian conclusions and not the controversial African ones end up in the abstract of the paper is also notable.

The pertinent portion of the paper addressing this point states:

The admixture profile of our dataset (2183 individuals from 61 populations genotyped for 40,272 SNPs; Supplementary figures S2 and S3, Supplementary Material online), based on ADMIXTURE analyses (Alexander, et al. 2009), shows that the Malagasy genetic diversity is best described as a mixture of 68% African genomic components and 32% Asian components, corresponding well with the results of previous studies (Capredon, et al. 2013; Pierron et al. 2014). While the African ancestry component in Malagasy appears to be broadly similar to that still present today in South African Bantu, the Asian ancestry presents a more complex pattern. . . . to more specifically identify the Asian ancestry of the Malagasy genome, we performed a Local Ancestry analysis with PCAdmix (Brisbin, et al. 2012) using two proxy parental meta-populations comprising 100 individuals with African ancestry (randomly selected from Yoruba, South African Bantu, Kenyan Luhya and Somali groups) and Asian ancestry (randomly selected from Chinese, Philippine Igorot, Bornean Ma’anyan and Malay groups). . . . To expand on this, however, we inferred the population sources of the Malagasy, their relative ratios and the dates of potential admixture events with GLOBETROTTER (Hellenthal, et al. 2014), defining each population in our dataset as a donor/surrogate group and the Malagasy as the recipient, using the haplotype ‘painting’ data obtained with Chromopainter (Lawson, et al. 2012). The best fit outcome for the Malagasy was obtained under a model of a single admixture event between two sources: the Banjar representing 37% of modern Malagasy and the South African Bantu population representing the other 63% (r2 =0.99, P<0.01; Figure 2 and Supplementary table S5, Supplementary Material online). The admixture event was dated to 675 years BP (95% CI: 625-725 years BP, Supplementary table S5, Supplementary Material online), which is similar to the dates of admixture estimated by ALDER (550-750 years BP) using Banjar population in combination with the South African Bantu (Supplementary table S6, Supplementary Material online)(Loh, et al. 2013). When each Malagasy ethnic group is analysed separately, similar parental populations, admixture proportions and dates are obtained with the noticeable older by guest on July 12, 2016 http://mbe.oxfordjournals.org/ Downloaded from estimated dates towards the east coast of Madagascar (Supplementary table S5, Supplementary Material online). Crucially, these dates of genetic admixture, in agreement with a previous study (Pierron et al. 2014), reflect the midpoint or end of noticeable admixture between groups of Asian and African ancestry in Madagascar, rather than the start of this contact. Therefore they could correspond to the end of the period of the main Austronesian presence in Madagascar that started around the first millennium CE (Dahl 1951, 1991; Dewar and Wright 1993; Adelaar 1995; Cox et al. 2012; Adelaar forthcoming). On the other hand, around 1100-700 years BP, climatic changes in the South of Africa forced Bantu populations to move to more hospitable places (Huffman 2000). This South Bantu migration has previously been suggested as an explanation for the higher density of populations observed in the South of Madagascar (Beaujard 2012a). As all of our sampled groups live in the South of Madagascar, and considering that the estimated dates of admixture are more recent on the west coast (Supplementary tables S5 and S6, Supplementary Material online), it is tempting to interpret our admixture date as marking the last significant Bantu migration to Madagascar, perhaps initiated by climatic changes in Africa.

Suffice it to say that the analysis of the African side of the genetic contribution is shallow and does not rigorously compare competing hypotheses of African contributions.

The Supplemental Materials indicate that the African samples other than South African Bantu come from International HapMap, et al. (2010) (i.e. Integrating common and rare genetic variation in diverse human populations. Nature 467: 52-58. doi: 10.1038/nature09298) and Pagani, et al. (2012) (i.e. Ethiopian genetic diversity reveals linguistic stratification and complex influences on the Ethiopian gene pool. Am J Hum Genet 91: 83-96. doi: 10.1016/j.ajhg.2012.05.015). The South African Bantu sample comes from May, et al. (2013) (Genetic diversity in black South Africans from Soweto. BMC Genomics 14: 644. doi: 10.1186/1471-2164-14-644).

Another data set of Southeastern Bantu speakers referenced in May, et al. (2013) seems to overlap with the Soweto sample and derives from Schlebusch, et al., "Genomic variation in seven Khoe-San groups reveals adaptation and complex African history." Science. 2012, 338: 374-379.

It is also possible that Soweto Bantus are very genetically distinct from Mozambique Bantus and may be more similar to ancestral East African Bantus than modern East African Bantus, because they may lack subsequent Nilo-Saharan Ancestry and may, in general have less of a substrate influence.

The abstract of the paper and its citation data are as follows:

Malagasy genetic diversity results from an exceptional proto-globalisation process that took place over a thousand years ago across the Indian Ocean. Previous efforts to locate the Asian origin of Malagasy highlighted Borneo broadly as a potential source, but so far no firm source populations were identified. Here, we have generated genome-wide data from two Southeast Borneo populations, the Banjar and the Ngaju, together with published data from populations across the Indian Ocean region. We find strong support for an origin of the Asian ancestry of Malagasy among the Banjar. This group emerged from the long-standing presence of a Malay Empire trading post in Southeast Borneo, which favoured admixture between the Malay and an autochthonous Borneo group, the Ma’anyan. Reconciling genetic, historical and linguistic data, we show that the Banjar, in Malay-led voyages, were the most probable Asian source among the analysed groups in the founding of the Malagasy gene pool.

Brucatol, et al., "Malagasy genetic ancestry comes from an historical Malay trading post in Southeast Borneo." 33 (7) Molecular Biology and Evolution (July 5, 2016).

The literature cited is as follows (and admittedly includes some other papers I haven't yet seen):

* Adelaar A. 2009a. Towards an Integrated Theory about the lndonesian Migrations to Madagascar. In. Ancient human migrations: a multidisciplinary approach.: University of Utah Press

* Adelaar KA. 1995. Borneo as a cross-roads for comparative Austronesian linguistics. In: Canberra AAEP, editor. The Austronesians: historical and comparative perspectives. p. 81–102.

* Adelaar KA. 2009b. Loanwords in Malagasy. In: Haspelmath M, Tadmor U, editors. Loanwords in the world’s languages: a comparative handbook. Berlin, Germany: De Gruyter Mouton. p. 717-746.

* Adelaar KA 1989. Malay influence on Malagasy: linguistic and culture-historical implications. Oceanic Linguistics 28: 1-46. doi: 10.2307/3622973

* Adelaar KA. forthcoming. Who were the first Malagasy, and what did they speak? In: Acri A, Landmann A, editors. Cultural Transfer in Early Monsoon Asia. Singapore: Institute of Southeast Asian Studies.

* Alexander DH, Novembre J, Lange K 2009. Fast model-based estimation of ancestry in unrelated individuals. Genome Research 19: 1655-1664. doi: 10.1101/gr.094052.109 by guest on July 12, 2016 http://mbe.oxfordjournals.org/ Downloaded from Beaujard P. 2012a. Les mondes de l’ocean indien. Vol. 2 : L’océan Indien, au cœur des globalisations de l'Ancien Monde (7e-15e siècles). Paris, France: Armand Collin. Beaujard P. 2012b. Les mondes de l’océan Indien. Vol. 1 : De la formation de l’État au premier système-monde afro-eurasien (4e millénaire av. J.-C.-6e siècle apr. J.-C.). Paris, France:

* Armand Collin. Brisbin A, Bryc K, Byrnes J, Zakharia F, Omberg L, Degenhardt J, Reynolds A, Ostrer H, Mezey JG, Bustamante CD 2012. PCAdmix: Principal componentsbased assignment of ancestry along each chromosome in individuals with admixed ancestry from two or more populations. Human Biology 84: 343-364. doi: 10.3378/027.084.0401

* Capredon M, Brucato N, Tonasso L, Choesmel-Cadamuro V, Ricaut F-X, Razafindrazaka H, Rakotondrabe AB, Ratolojanahary MA, Randriamarolaza L-P, Champion B, Dugoujon J-M 2013. Tracing arab-islamic inheritance in Madagascar: Study of the Y-chromosome and mitochondrial DNA in the Antemoro. PLoS One 8: e80932. doi: 10.1371/journal.pone.0080932

* Cox MP, Nelson MG, Tumonggor MK, Ricaut F-X, Sudoyo H 2012. A small cohort of Island Southeast Asian women founded Madagascar. Proceedings of the Royal Society B: Biological Sciences 279: 2761-2768. doi: 10.1098/rspb.2012.0012

* Dahl OC 1951. Malgache et maanjan: une comparaison linguistique. Oslo, Norway: Edege-Intituttet.

* Dahl OC 1991. Migration from Kalimantan to Madagascar. Oslo, Norway: Norwegian University Press : Institute for Comparative Research in Human Culture.

* Dewar RE, Wright HT 1993. The culture history of Madagascar. Journal of World Prehistory 7: 417-466. doi: 10.1007/BF00997802 by guest on July 12, 2016 http://mbe.oxfordjournals.org/ Downloaded from Fourquet R, Sarthou J, Roux J, Aori K 1974. Hemoglobine S et origines du peuplement de Madagascar: nouvelle hypothese sur son introduction en Afrique [Hemoglobin S and origins for the settlement of Madagascar: new hypothesis on its introduction to Africa]. Arch. Inst. Pasteur Madagascar 43: 185–220.

* Fuller DQ, Boivin N, Hoogervorst T, Allaby R 2011. Across the Indian Ocean: the prehistoric movement of plants and animals. Antiquity 85: 544-558.

* Hellenthal G, Busby GB, Band G, Wilson JF, Capelli C, Falush D, Myers S 2014. A genetic atlas of human admixture history. Science 343: 747-751. doi: 10.1126/science.1243518

* Hewitt R, Krause A, Goldman A, Campbell G, Jenkins T 1996. beta-globin haplotype analysis suggests that a major source of Malagasy ancestry is derived from Bantu-speaking Negroids. Am. J. Hum. Genet. 58: 1303–1308.

* Huffman TN. 2000. Mapungubwe and the origins of the Zimbabwe culture. In: Leslie M, Maggs T, editors. African naissance: The Limpopo valley 1000 years ago. Cape Town, South Africa: South African Archaeological Society. p. 14-29.

* Hurles ME, Sykes BC, Jobling MA, Forster P 2005. The dual origin of the Malagasy in Island Southeast Asia and East Africa: evidence from maternal and paternal lineages. Am J Hum Genet 76: 894-901.

* Kusuma P, Brucato N, Cox MP, Pierron D, Razafindrazaka H, Adelaar A, Sudoyo H, Letellier T, Ricaut F-X 2016. Contrasting Linguistic and Genetic Influences during the Austronesian Settlement of Madagascar. Scientific Reports 6:26066. doi: doi: 10.1038/srep26066

* Kusuma P, Cox MP, Pierron D, Razafindrazaka H, Brucato N, Tonasso L, Suryadi HL, Letellier T, Sudoyo H, Ricaut F-X 2015. Mitochondrial DNA and the Y by guest on July 12, 2016 http://mbe.oxfordjournals.org/ Downloaded from chromosome suggest the settlement of Madagascar by Indonesian sea nomad populations. BMC Genomics 16: 191. doi: 10.1186/s12864-015-1394-7

* Lawler A 2014. Sailing Sinbad's seas. Science 344: 1440-1445. doi: 10.1126/science.344.6191.1440

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Evidence Increasingly Rules Out Light Sterile Neutrino Hypothesis

The Standard Model of Particle Physics includes three flavors of neutrinos - electron neutrinos, muon neutrinos and tau neutrinos, so named because particle physicists weren't feeling particularly creative when they were hypothesized (and ultimately discovered).

There needs to be a neutrino counterpart to each charged lepton to preserve the approximate lepton flavor conservation symmetry of the theory (neutrino oscillation prevents it from being a perfectly conserved symmetry), and weak force boson decays have long confirmed that there are three flavors of weakly interacting neutrinos, so three flavors of neutrinos are necessary to make electroweak theory conform to observation.

Anomalies in reactor neutrino data had suggested the possibility of a fourth light neutrino that oscillates with the three ordinary neutrinos, but do not interact via the weak force.

The cosmologically measured constant Neff (effective N) for the number of neutrino flavors increasingly disfavors a fourth type of neutrino that the existing three flavors oscillate with (but which does not interact via the weak force). So do new cosmological data bounds on the sum of the mass of all neutrino flavors because the difference between the maximum value of the sum of the masses of the three neutrino flavors and the minimum value derived from the differences in mass between the three primary neutrino mass states is increasingly small, placing an upper bound on the mass of any fourth sterile neutrino.

(Note, however, that the cosmology purposes, a neutrino with a mass far in excess of 1 eV/c^2 such as a sterile neutrino with a mass on the order of a keV, which has been proposed as a dark matter candidate, is outside the cosmology definition of a neutrino. The cosmology definition is largely synonymous with the definition of "hot dark matter", rather than using the usual Standard Model definition.)

This year's Neutrino 2016 Conference has produced three papers all documenting new experimental findings the strongly disfavor the kind of sterile neutrino that is light enough and mixed enough with the other three neutrino flavors to explain the apparent reactor neutrino anomalies that had prompted the light sterile neutrino hypothesis. One of the papers setting for the new experimental limits is based on data from the Daya Bay experiment, one is based on MINOS data, and one combines data from the Daya Bay, MINOS and Bugey-3 experiments to obtain a global exclusion based upon the latest data.

Taken together, the cosmology and earth based experimental exclusions provide a strong and robust exclusion of the light sterile neutrino hypothesis in all circumstances in which any other evidence might have suggested it in the first place (and the reactor anomaly itself have also grown less acute as more data and analysis have examined it).

Also, the titles and abstracts of the papers on neutrinoless double beta decay this year make clear that nobody has credibly observed neutrinoless double beta decay yet experimentally, so the experimental minimum bound on the potential mean time frame of neutrinoless double beta decay continues to get incrementally longer from the last time this data was reported.  No instances of lepton number violation have been observed in any other context either.

Gravitationally Bound Composite Neutrino Structures?

The following abstract describes a poster presentation at the Neutrino 2016 Conference that is currently in progress (July 4-9) in South Kensington, England:

Poster session 3 – Wednesday 6 July

P3.037 Gravitationally confined relativistic neutrinos

C Vayenas1,2, A Fokas3,4 and D Grigoriou1

1University of Patras, Greece, 2Division of Natural Sciences, Greece, 3University of Cambridge, UK, 4University of Southern California, USA

Combining special relativity, the equivalence principle and Newton’s universal gravitational law with gravitational rather than rest masses, one computes that gravitational interactions between relativistic neutrinos with kinetic energies above 10 MeV are very strong and can lead to formation of gravitationally confined composite structures. One may model the formation of such composite structures by considering three neutrinos moving symmetrically on a circular orbit under the influence of their gravitational attraction, and by assuming quantization of their angular momentum, as in the Bohr model of the H atom. The model contains no adjustable parameters and its solution leads to composite state radii close to 1 fm and neutrino velocities so close to c, that the corresponding Lorentz factor, gamma, values are of the order of 5*10⁹. 

It is thus found that when the neutrino rest masses are of the order of 0.05 eV/c2, then the mass, 3(gamma)m_o, of such three rotating neutrinos structures is very similar to that of hadrons (~ 1 GeV/c2). The thermodynamics of the phase condensation of neutrinos to form such structures are compared with QCD calculations for the quark-gluon condensation temperature.

Using the same approach we find that the mass of relativistic rotating Ve – e+/- pairs is 81 GeV/c2, close to that of W+/-bosons.

The W boson coincidence is particularly interesting.  Another interesting poster considers a possible gravitational source for neutrino mass.

Boya and Rivera have reviewed a number of similar theories.