Tuesday, July 31, 2012

Dienekes' Estimates Of Y-DNA Clade Ages

Armed with new and improved software, methodologies and data, Dienekes' has produced his own estimates of the ages of various Y-DNA haplogroups.   I summarize Dienekes' date estimates for Y-DNA haplogroups below with somewhat less technical detail and some more descriptive context from the overall phylogeny of the Y-DNA haplogroups (upon which there is a nearly complete consensus as to locations on a branching tree of descent, although there is not a consensus as to the age and the place of origin of the clades). 

His knowledgeable amateur estimates (his day job is in the IT industry in Greece) are generally in line with previous estimates from published journals.  Also, note that many of the gaps in his estimates to date (which he is rapidly filling) are strongly constrained and predicted by estimates for parent clades, daughter clades and sister clades, and that there are estimates in the literature for these clades, just not estimates within the last couple of days from Dienekes as part of a coherent effort.  The most interesting gaps in the estimates are those for D, G, H, L and T which have the weakest analogs and bounds from the estimates that Dienekes has made so far.

I analyze the issue of the calibration of the Y-DNA genetic based date estimates after recapping his results below.  I also note briefly that the one outlier in his estimates is C1-C3 which one would expect for a variety of reasons to be much older. Analysis of what the dates themselves imply about human prehistory and the differences in the conclusions that I draw from the data compared to those drawn by Dienekes will have to wait for another post or posts.  (See also my November 2010 post at Wash Park Prophet addressing similar issues with quite a bit of reference to the literature.)

Y-DNA Clades, Comparison Ages (in years ago), and Description of Clade.

Y-DNA Adam.  159,298 This is the most recent common male ancestor of all modern humans.
*BT 71,188 The clade that breaks off from the mostly Paleo-African A.
**CT 62,439 Shared root of DE and CF from African B. 

DE 62,205 The source of Asian D & African E. A few basal cases found in both areas.
*D Sporadic Asian distribution (e.g. Andaman Islands, Japan, Tibet).  No estimate yet (less than DE).
*E 57,703 The root of this African clade with migrant branches in West Eurasia
**E1b1 43,587 The predominant sub-haplogroup of E in Africa esp. outside E. Africa.
***E1b1b1a1 13,817-19,482A leading West African clade.

CF 47,379 Root of all predominantly non-African clades except D.
*C1-C3 25,022 Mostly Southern Asian.
*F West Eurasian rooted branches are from F as are many Asian ones. No estimate yet (less than CF and more than IJK)
**G Mostly European/Caucasian branch of F.  No estimate yet (less than CF, similar to IJK)
**H Mostly South Asian branch of F.  No estimate yet (less than CF, similar to IJK)

IJK 41,910 Root of IJ and K.  Derives from F.
*IJ 35,589 Root of I and J.
**I 26,885 West Eurasian, possibly predominant in European Paleolithic
***I2a1 19,513 Mostly Central and Eastern European
**J 24,497 West Eurasian. J1 is mostly Semitic (see below for J2).
***J2 23,420 Highland West Asian root probably spread by Indo-Europeans.
* K-M9 36,389 Root of MNOPS and LT as well as other K clades.

LT Derived from K.  No estimate yet (less than K)
*L Generally Indus Valley.  No estimate yet (less than LT).
*T Broad West Eurasian and North and East African distribution.  No estimate yet (less than LT)

MNOPS Derived from K. No estimate yet (less than K, more than NO and P)
*M Southern Asian. No estimate yet (less than K and similar to NO and P)
*NO 32,467 An Asian branch of MNOPS.
**N Northern Asian.  No estimate yet (should be similar to O).
**O 26,145-27,870 Mostly Southern Asian. See [Note 1]
***O3a1-O3a2 18,765 Northern Asian.
*P 33,043 Central and South Asian.  Sister clade to NO. 
**Q North Asian and Americas.  Descendant of P.  No estimate yet (less than P)
**R West Eurasian.  Descendant of P.  No estimate yet (less than P and more than R1)
***R1 23,657 A predominant European haplogroup.
****R1b1a2a1a1a5 6,476 About 25% of (mostly) Western European haplogroups within R1b.
***R2 Generally Indus River Valley.  No estimate yet (similar to R1)
*S Melanesian. No estimate yet (less than K, similar to NO and P)

[Note 1]: "This haplogroup [O] appears in 80-90% of most of populations in East Asia and Southeast Asia, and it is almost exclusive to that region: M175 is almost nonexistent in Western Siberia, Western Asia, Europe, and Africa and is completely absent from the Americas, although certain subclades of Haplogroup O do achieve significant frequencies among some populations of South Asia, Central Asia, and Oceania."  Sub-branches of haplogroup O have strong language family associations.

The Case That His Estimates Need To Be Calibrated To Be 50% Longer

His estimates using the methods he is using, like the estimates in most published academic work, are low compared to the estimates one would make looking at the more definitively dated archaeological record.

A date about 50% higher would be a better fit to the archaeological evidence of modern humans which has been estimated at as much as 250,000 years ago. A 50% higher date also seems to be a better fit for DE and CT which should match the Out of Africa date which archaeologically is closer to 100,000 years ago than 62,000 years ago. This would also put the sister clades of MNOPS closer to the archaeologically supported date of around 45,000 for Melanesia and one would expect the sister clade NO to have an age similar to Melanesian S. A 50% longer date would have I coincide with the modern human settlement of Europe, which would be a more likely date than one six thousand years before the Last Glacial Maximum in the Upper Paleolithic. This would put the most common haplogroup of R1b in Western Europe in the Holocene, fairly close in time to earliest ancient DNA evidence of modern mtDNA haplogroups like H in Europe and North Africa, although the shorter estimate would be a fit to the European Copper Age which would also make some sense.

A recalibration of Y-DNA dates would also bring Y-DNA haplogroup age estimates more closely in line with age estimates of mtDNA haplogroups that very likely came into being and spread with corresponding Y-DNA haplogroups.  For example, a common estimate for the most recent common maternal ancestor of all modern humans is 200,000 years ago: "In 1987, Cann et al. suggested that mitochondrial Eve may have lived between 140-280 thousand years ago." While, mitochondrial Eve and Y-DNA Adam don't have to have been contemporaries, a 40,000 years spread between the two seems unlikely. The mtDNA estimates for characteristic Out of Africa mtDNA haplogroups are also a bit short relative to the archaeological evidence of humans leaving Afica, but by a lesser amount. Increasing conventional mtDNA estimates by about 20% brings them better into line with the archaeological evidence.

In short, I suspect, given the comparable percentage of mismatch of archaeological dates that ought to correspond with Y-DNA genetic based dates, that the entire scale is miscalibrated and should be about 50% longer, give or take (all of these estimates have meaningful margins of error).

Since Y-DNA estimates are derived from number of generations and then converted to years, generally based on an assumption of a 25 year generation, a recalibration of the data could result from something as simple as the historical average generation length being closer to 17 years than 25 years, which honestly makes more sense in an environment in which there would be no meaningful contraception and no capacity to segregate young adult women from men for many years.

If I recall correctly, the 25 year generation length has ethnographic roots in modern hunter-gather generation length, but the modern hunter-gatherers live in marginal areas where there may be a tendency towards longer generations, while Paleolithic hunter-gatherers would have lived in prime territory that would have made shorter generations feasible. This recalibration may not be equally valid for R1b1a2a1a1a5, however, since it, unlike all of the other dates, derives mostly from people living a food producing life, rather than people living a hunting-gathering life.

NOTE: Repeatedly updated for accuracy, clarity, and formatting on July 31, 2012.

Thursday, July 26, 2012

Spanish Baby Snatching

A Spanish Civil War era scheme that continued until the 1990s where almost 300,000 "Red" women's babies were stolen from them shortly after delivery and placed in conservative families in an effort to make their children more conservative and reshape the nation is starting to be unraveled.

This was one of the grandest nature v. nuture experiments in modern history, although the results are unknown and the methods violated every principle of experiments on human subjects.

Monday, July 23, 2012

A Theoretical Basis for 2H=2W+Z?

A Quantum Diaries Survivor has a guest post offering up a theoretical justification for a Higgs boson mass exactly equal to one half of the sum of the masses of the three weak force bosons.

Proponent Ashay Dharwadker argues that he and a colleague have developed a true Grand Unified Theory, maybe even a Theory of Everything, that approximates the Standard Model and general relativity with almost no beyond the Standard Model physics. It isn't the first time I've seen the proposal discussed, although arguably it is the most respectable. This should be incredibly exciting and even transformative, and the fact that it doesn't seem to be suggests room for some healthy skepticism. But, it is worth a look one of these days.

Posting Drought Forecast

This year is one of the driest years in Colorado, which is at the epicenter of a drought that covers most of the continental United States, since the 1950s and the Dust Bowl of the 1930s.  Posting volume at Dispatches from Turtle Island, your Denver based science blog, may be similarly scarce for a while due to a variety of impositions on my time.

This blog has not been abandoned, however, and I expect to make regular posts on the usual topics at a more subdued volumes over the next few months.

Thursday, July 19, 2012

Heavy WIMPS Experimentally Excluded Again

The latest results from Xenon100s direct search for dark matter has ruled out heavy WIMPs (dark matter in the form of weakly interacting massive particles) in the vincinity of Earth down to something less than 55 GeV for even very slight interaction cross sections (2*10^-45 cm^2) and ever so slightly more interacting dark matter particles from about 15 GeV to 1 TeV of mass (almost the entire WIMP mass range in cold dark matter theories).  It has ruled out somewhat more strongly interacting WIMPs down to masses of about 5 GeV.  Basically, anything heavier than a bottom quark is ruled out.

A twelve megabyte file size paper on the results can be downloaded here.  The money chart, showing the exclusion range for all published direct dark matter detection experiments is on page 50 (the second to last page).

The Bottom Line In The Context Of Other Dark Matter Detection Experiments

The Xenon100 results for 2012 exclude almost the entire range of almost a dozen previous direct dark matter detection experiments, with the Xenon 10 results from 2011 providing some additional exclusions for particles of 5 GeV to 8 GeV masses with fairly high cross-sections of interaction (10^-41 cm^2 to 10^-40 cm^2). 

In particular, Xenon100's results confirms prior studies ruling out dark matter with 8 GeV to 12 GeV and contradicts prior studies (COGENT, DAMA/Na and CRESTT-II) that had suggested that there might be dark matter particles of those masses, although with not entirely consistent and fairly strong cross-sections of interaction. 

Also, the nature of these experiments is that it is easy to overlook a tiny but easily explained contribution to background noise in the detector that looks like but does not actually constitute a real dark matter detection event. This entire class of experiments is inherently biased towards false positives due to experimenter error.

Considering Xenon 100 Together With Collider Experiment Data

The Xenon100 data is a nice complement to the LHC data.

The under 15 GeV masses where some direct detection of dark matter experiments have not ruled out the presence of some kind of dark matter with a very slight cross section of interaction (which other experiments contradictorily say that they have ruled out) are well within the mass sensitivity range of current collider experiments like the LHC and prior ones like Tevatron and the LEP to direct directly through entirely different methods.  Precision electroweak decay data pretty much completely rules out the possibility of any weakly or electromagnetically interacting particle in that mass range, since otherwise more W and Z bosons would have more "missing energy" than the amount actually observed which is currently fully and very exactly explained by Standard Model neutrinos. 

It is coinceivable that collider experiments would miss, but direct detection of dark matter experiments might detect "sterile neutrinos" that interact via gravity and Fermi contact interactions, but not via the weak force or electromagnetic force or the strong force.  But, sterile neutrinos that don't interact via the weak force would not be expected to have as large of a cross-section of interaction of the one suggested by to possible by the results from COGENT, DAMA/Na, and CRESTT-II. 

To slightly overgeneralize, the heavier a dark matter particle that is a WIMP is, the easier it is for Xenon100 to see it, even if it has a very slight cross-section of interaction (and has some resolution down to the tens of GeV or even the high single digit GeV).  In contrast, LHC and prior collider experiments are good at seeing light particles, but start to lose detection resolution in the hundreds of GeVs range or higher (cutoffs vary with hypothetical particle properties).  The lighter a particle is, at least down to the hundreds of KeV mass range (and up to at least the 45 GeV or so if it interacts via the weak force at all as all known fundamental fermions and fundamental bosons with mass do, and none of the fundamental bosons without mass do), the easier it is for collider experiments to detect it.

Since their sensitivity ranges, in terms of particle masses, now overlap with each other, the two classes of experiments combined effectively rule out non-Standard Model particles in any mass range that has been considered seriously in and dark matter theories that credibly addresss the phenomenology.

Other Limitations on Dark Matter Properties.

Experimental astronomy data looking at dark matter effects in particular galaxies and galaxy clusters places bounds dark matter particle speed, mass and interaction cross-sections, as do models that try to reproduce the large scale structure of the universe on dark matter distribution and behavior. 

The data from astronomy currently seems to favor lighter, faster moving particles called "warm dark matter" in the KeV mass range (which none of the direct dark matter detection experiments are theoretically capable of observing), rather than hundreds of GeV masses favored by older "cold dark matter" theories that are increasingly at odds with the evidence from astronomy, and "hot dark matter" theories that posit that dark matters are simply ordinary neutrinos behaving in well understood ways and produced via the weak force decays of energetic particles (thereby making them move at close to the speed of light).  Cold dark matter models produce more small galaxy scale structure than we observe; warm dark matter produces less large scale structure in the universe than we observe.

Sterile Neutrinos Or Bust.

Basically, at this point, we are in a light sterile neutrinos of bust situation when it comes to non-Standard Model dark matter particles.  The theoretically well motivated alternatives to a sterile neutrino have been mostly ruled out by experimental data and astronomy observations, while beyond the Standard Model theories with sterile neutrinos (aka right handed neutrinos) that weigh more than regular neutrinos (and hence would move slower on average), are common place, since there are right and left handed versions of all fermions other than neutrinos.

FWIW, I have real doubts about whether not yet discovered, non-baryonic dark matter particles are out there at all, at least in the vicinity of the solar system.  They probably don't exist either.  But, if undiscovered kinds of dark matter particles are out there, sterile neutrinos do seem to be the best hypothetical particle candidates out there.

Not Encouraging For SUSY

In particular, this is bad news for SUSY which is independent of (1) non-detection of SUSY at the LHC, and (2) the non-detection of neutrinoless double beta decay at levels predicted for high characteristic energy scale SUSY theories which have not yet been ruled out by the LHC, because one of the most important phenomenological motivations for SUSY theories that is shared generically by almost all SUSY theories is that they provide a heavy WIMP dark matter candidate.  In general, the higher the characteristic energy scale of a SUSY theory, the heavier its lightest stable supersymmetric particle is expected to be.   So, the part of the SUSY parameter space not excluded by the LHC yet should provide the easiest for direct dark matter detection experiments to detect WIMPs.

If there is no dark matter in this mass range, then all of the SUSY theories that predict stable lightest supersymmetric particles (LSPs) in that mass range are again disfavored by the experimental data.  I have yet to see a SUSY theory that predicts a lightest supersymmetric particle of 15 GeV of mass or less, for the simple reason that collider experiments should have detected such a light LSP long ago.  Even strong SUSY proponents concede that SUSY particles that light have been experimentally excluded even in non-minimal supersymmetry theories.

Of course, this result doesn't rule out SUSY theories with no stable supersymmetric particles, but theories with no stable supersymmetric particles have one less point of phenomenology explained to recommend and empirically motivate them.  Why have a SUSY theory that can't even provide one viable dark matter candidate out of its embarassment of riches when it comes to new particles?

Koide's Formula and Running Fermion Masses

One of the criticisms that Lubos Motl has directed towards Koide's formula (which in its original form shows that the sum of the three charged lepton masses divided by the square root of the sum of their squares is exactly two-thirds, midway between the minimum 1/3rd value of that ratio and the maximal 1 value of that ratio) is that in its naiive version it, one uses a not particularly fundamental definition of mass (the real valued rest mass of the energy level of that particle).  Motl would personally favor using a complex valued "pole mass" in any fundamental formulation of mass relations in the Standard Model, but hasn't tested that approach to see if it would produce a different result.

One way to see if this criticism has any substance to it is to apply Koide's formula to lepton and quark triples that have been proposed to be Koide triples and to see if the formula is substantially distorted by the running of quark and lepton masses at different energy levels. 

Koide's himself wrote one of the seminal papers calculating these running masses at various energy levels in 1998, and it was updated to reflect more recent experimental measurements and more energy levels in 2008.

While the masses of quarks and leptons respectively due "run" with the energy level of the interaction in which they are measured, this has far less of an impact on the relative masses of particles within a particular Koide triple than it does on the absolute values.  So, it is not obvious that the formula fails to fit the facts by anything more than the inherent uncertainty in the experiments measurements available to check it against, when differently defined particle masses are involved.

Given the rather large uncertainties with which we know the quark masses, I suspect that the running of the mass values for quarks won't have much of an impact on the validity of Koide's formula for these triples.  The quoted uncertainty in the strange quark mass, for example, is on the order of 20-30%.

The charged lepton masses provide a sterner test as they are known with much more precision.  But, they do seem to run at rates closely (if not exactly) to proportionate to the energy scale involved. 

A Few Calculations

For example, the running electron, muon and tau masses are each not quite 2% lower at the energy scale of a top quark than they are at the energy scale of a charm quark (which is about 138 times smaller than a top quark, give or take).  Similarly, the masses of the charged leptons between the Fermi scale (the Z boson mass energy level of 91.2 GeV) and the GUT scale (2*10^16 GeV) each declines, to three significant digits anyway, by a factor of 3.60% over fourteen orders of magnitude of running mass distortion.  And, since Koide's formula is true independent of the units of mass used, any proportionate adjustment of all of the charged lepton masses should be immaterial to its accuracy.

There are more elegant ways to show this, I am sure, from direct comparison of the running mass renormalization equations themselves, but suffice it to say that it is safe to assume that Koide's formula should continue to hold true to a quite high degree of precision in any consistently applied redefinition of the charged lepton masses.

Put another way, Koide's formula is an empirical one that seems to hold to a high degree of precision but has not really deep theoretical basis, so it is hard to know what definitions of mass to use in a deeper theoretical framework that reproduces the Standard Model with fewer fundamental constants and some deeper relationships between the constants that are now known. 

But, any definitions that produce the same relative masses of the charged leptons as the most commonly used version of his formula should produce the same result, any there are many alternative defintions of those masses in which this is the case.

A Footnote on the Precision of What We Know About The SM Constants.

We have some experimental estimates for each of the Standard Model constants except the CP violating phase of the PMNS matrix (i.e. a term that would make neutrino and antineutrino oscillation rates asymmetrical in carefully constucted circumstances).  Some of these constants, like the proton and neutron mass, the charged lepton masses and the electromagnetic couple constants (including the running of that constant at sub-TeV levels) are measured with extreme precision.  But, some of those constants like the absolute neutrino masses and oscillation constants and the strange quark mass are constants for which we have only very approximate values.  The values of the CKM mixing matrix entries are known with considerable precision, while the values of equivalent matrix for leptons are know only at a one or two significant digit level of accuracy for the most part and a great deal of published work that tries to make calculations involving neutrino oscillations use theoretically suggested approximations instead of experimentally measured values.

Also, since the masses of quarks other than the top quark cannot be measured directly, since the other five quarks are never observed outside of composite multiquark hadrons bound by gluons and many of the measurements are only available in high energy physics interactions, all of these constants are highly theory dependent.

Theorists have confidence that the QCD Lagrangian and numerical approximations of it derived from it and selective measurement of QCD constants at high energies are correct and can be extrapolated to lower energies.  And, generally speaking the agreement between theory and experiment has been excellent.  But, imprecision in both the experimental values and the numerical calculations of theoretical predictions from first principles means that few QCD measurements, particularly in lower energy systems, are accurate to much more than two significant digits, which leaves considerable room for introducing tweaks to the Standard Model QCD formulas without doing any injustice to current experimental knowledge.  Indeed, even gross simplifications of the Standard Model formulation, such as the assumption that up, or both up and down quarks are massless, that they are fewer than six or even as few as four quarks, are routinely used to improve computational ease in numerical QCD calculations that aren't particularly sensitive to these constants.

Similarly, the "beta functions" that govern how the electromagnetic, weak and strong force coupling constants run at different energy levels are all extrapolated from fairly thin data, which is particularly thin at the highest energy levels, without any direct experimental confirmation that they are correctly formulated for energy levels many orders of magnitudes higher than any experiment has every measured (a span of about thirteen orders of magnitude between experiment and the GUT scale).

Monday, July 16, 2012

SUSY Stop Quark Signals At LHC?

Lubos Motl (a strong SUSY believer) is trumpeting experimental results at the LHC's CMS experiment and ATLAS experiment that he argues each show 2.5 sigma signals of 300 GeV stop quarks in the same detection channel, the supersymmetric boson that is the partner of the top quark and often expected to be the lightest of the superpartners of the Standard Model fermions.   Motl acknowledges, however, that neither CMS nor ATLAS are interpreting the overall results to be a meaningful stop quark signal as he does.

The ATLAS experiment powerpoint presentation (cited by SUSY skeptic and Motl nemesis Peter Woit) at the same conference that Motl discusses, however, dismisses this conclusion and instead argues that the experimental data are consistent with the Standard Model and show results in at least one channel that rules out a 300 GeV stop quark for most values of the relevant additional parameter that influences the expected signal at the 95% confidence level.

At least twenty-nine papers discussed SUSY prospects at the LHC (and in relation to that the utility of a new international linear collider for studying these issues). More of the papers discussed SUSY to some extent even though their titles don't disclose this fact. Most of the rest of the papers were purely experimental in orientation. No other specific class of theories had even two papers discussing it. SUSY variants remain the only really respectable, widely evaluated alternative to the plain vanilla Standard Model in beyond the Standard Model high energy physics.

Many proposals with expanded Higgs boson sectors are ruled out, but certain models with both singly and doubly charged Higgs bosons in addition to the Standard Model Higgs boson (Georgi-Machacek Model triplets), are not ruled out by the LHC data alone although they are disfavored by the Tevatron data.

Possible BSM values in the Standard Model CKM mixing matrix (potentially making it impossible to fit the model to the data because it is overconstrained) disappeared with more precise measurements from LHC.

Arabian Paleoclimate In A Nutshell

Ask questions, get answers from a blog commenter who is actually a professional in the relevant field.


"During what windows of time expressed in terms of years ago, would Arabia have been habitable for terrestrial Paleolithic hunter-gathers? Was there more than one in the last 150,000 years or so?"

There are several episodes of varying magnitude that have left a "pluvial" imprint on the landscape (e.g., speleothem growth, lacustrine sediments, wadi aggradation, etc...). Perhaps most surprisingly, an ancient lake deposit in Sharjah, of several meters accumulation, has recently been dated to the middle of MIS 6 (~160 - 150 ka BP). This may have been the initial priming of the pump that drew the first AMH wave of Fayans into Arabia (pardon the term, couldn't think of anything else to call these ambiguous people).

Easily the clearest and strongest pluvial signal comes during the Last Interglacial, ~130 - 120 ka BP. Although not pronounced, the section at Aybut Auwal shows subsequent wadi activation around MIS 5c (~110 - 100 ka BP). MIS 5a (~85 - 75 ka BP) is the last gasp of heightened precipitation before the onset of rapidly deteriorating conditions associated with MIS 4.

There is new evidence about to be published for a return to wetter conditions between roughly 60 - 55 ka BP. From my perspective, this period is particularly important by enabling bottlenecked communities within Arabian refugia to re-expand. In particular, there may be cultural connections between South Arabia and the southern Levant around this time. What is so attractive about this explanation (imo) is that it would finally explain from where the mysterious Initial Upper Palaeolithic in the Levant actually came. Since its discovery in the late 70s, nobody has ever sufficiently explained the origins of the core reduction technology seen at Boker Tachtit or Ain Difla. Why, suddenly, the emphasis on distal preparation of Levallois point cores? Sounds kind of Nubian-ish to me...

Continuing with the pluvial chronology: it used to be accepted that there was another wet phase in the middle of MIS 3 (~40 - 30 ka BP); however, there is now doubt about these old C14 dates. The verdict is still out for this timeframe.

Finally, rainfall begins to picks up again around 12 ka BP, at the onset of the Holocene Climatic Optimum. So, there are several windows of opportunity for expansion into Arabia (see Rosenberg et al. 2011). It is important to keep in mind that there were probably demographic expansions during every one of these windows, and not necessarily only coming from one source in East Africa. Imagine groups moving every which way, coming and going from all directions. After all, these are highly mobile hunter-gatheres we are talking about. Moving is what they do best.
One one hand, the fact that there have been  perhaps seven times that Arabian Empty Quarter has been habitable in the last 160,000 years is pretty remarkable, given that this is one of the most harsh deserts in the world right now.

On the other hand, these are short, five to ten thousand year wet spells interrupted by ten to twenty thousand years long dry spells. This is not a scenario in which you would expect to see long run cultural continuity and at the end of each wet spell you have to ask, did they go somewhere else or die out?

This summary also makes the Toba erruption, which coincides with the beginning of MIS 4's " rapidly deteriorating conditions" look like a real push factor in one of the likely locations for a modern human refugium in the Mesolithic, and not just an inconvenience and life style adjuster, although he does state:

[W]ere we lucky hunter-gatherers in the right place at the right time during the Last Interglacial, or crafty beachcombers struggling for survival across the post-apocalyptic post-Toba landscape? Pushed out of Africa, or pulled into Arabia? In my mind, this is the real disparity between the two models.

Interestingly, all of the Palaeolithic archaeologists working in Arabia unanimously agree on the "lucky hunter-gatherers" MIS 5 scenario.

50 Paleolithic Pathway Paradigms

There is an emerging consensus regarding important parts of the story of how modern humans populated the world during the Paleolithic era.  I recap the facts as I understand them, with no more specificity than widely held scientific views seem to support, in this post.

Modern Humans Evolve In Africa from Great Apes; Archaic Hominins Emerge From Africa

1.  In Africa, modern humans evolved on a branch of the great apes whose closest living relatives are the chimpanzee and the bonobo.  Intermediate hominins evolved from these great apes, probably including species that were evolutionary "dead ends" including (to the extent that they did not admix with modern humans), non-African Homo Erectus and Neanderthals.  There are something like half a dozen proposed African intermediate archaic hominin species in at least two or three genus level classifications although the precise species classification of individual specimens, and the relationships of these specicies to each other are disputed since the evidence is often fragmentary and isolated.

2. All Eurasian hominins have ultimate evolutionary origins from the same proto-hominin ancestor in Africa as that of modern humans who was most closely related to the chimpanzee and the bonobo.

3.  Modern humans were not the first species of hominin to leave Africa.  Homo Erectus was the first hominin to leave Africa and first appeared out of Africa around two million years ago, give or take a couple of hundred thousand years.

4.  Sometime around 250,000 years ago (with fairly wide error bars on that date), the most recent common ancestor of all modern humans evolved somewhere in Africa.  Estimates of this date from archaeological evidence and different methods of mutation rate driven genetic estimations are not identical, but are consistent with each other to margins of error on the order of plus or minus 50,000 year. 

5.  Modern humans evolved after Homo Erectus and Neanderthals evolved.  Modern humans are not directly ancestral, except due to two or more introgressions of archaic hominin DNA none of which is common to all modern humans, to Homo Erectus, to Neanderthals, to Denisovians (whatever species they may belong to), to the Homo Florensis.

6.  At the time the first modern humans left Africa there had been Homo Erectus and Neanderthals in Eurasia before them, and there may have been other or intermediate or hybrid archaic hominin species as well.  No hominins, however, had ever reached Australia or the Americas or Antactica or Oceania, before moder humans did.

Modern Humans Leave Africa

7.  Modern human initially migrated out of Africa via either Yemen or the Sinai Pennisula or both, Modern human did not make their original emergence out of Africa via Spain and not via direct ocean or sea travel to anywhere else.  It follows, of course, there there were modern humans in Southwest Asia before there were modern humans anywhere else outside of Africa. At the time that modern humans migrated out of Africa, Neanderthals were present in the Levant and Europe. 

8.  The oldest hominin remains widely accepted as being anatomically modern human outside Europe are at least 100,000 years ago.  There are stone tools in non-coastal Arabia from an era when that was not a desert that show strong commonalities with stone tools from the Nile Basin at the same time from thousands of years earlier.  There appear to be a wealth of stone tools, probably but not definitively associated with modern humans (they could have been Neanderthal tools) in this interior Arabian basin dating from sometime in the MIS 5 interglacial period which began ca. 130,000 years ago.  There is no archaeological evidence for modern humans outside African more than 130,000 years ago and there is nothing in mutation rate based genetic dates that demands an out of Africa date that old.

9.  There is dispute between moderns in which (1) there was an Out of Africa that failed wave starting sometime around 130,000 to 100,000 years ago in Southwest Asia, possibly without penetrating much further, and ending 75,000 years ago, followed by an Out of Africa wave that took hold 60,000 to 50,000 years ago, and in which (2) the first Out of Africa wave ca. 130,000 to 100,000 years ago was successful and is in continuity with all subsequent non-African populations with the archaeological evidence of modern humans gap from about 100,000 to 75,000 years ago being due either to poor preservation of modern human artifacts and remains, or to relocation of proto-Eurasians to non-Levantine refugium(s) including potentially the Nile Basin, the Horn of Africa, interior Arabia, the Persian Gulf, Iran, and South Asia that remain largely undiscovered at this time.  Neither theory is inherently inconsistent with minor subsequent Out of Africa waves of migration, although this possibility doesn't receive wide attention.

10.  All modern humans with recent origins outside of Africa have a low and fairly consistent percentage of Neanderthal admixture in their autosomal genome.  Neanderthal admixture is absent from modern humans with no ancestors outside of Africa.  The specific Neanderthal genes seen in East Eurasians and the specific Neanderthal genes seen in West Eurasians overlap only slightly due to some combination of parallel and similar, but separate, admixture events in a proto-West Eurasian and a proto-East Eurasian population, schism of an admixed proto-Eurasian population before admixed Neanderthal genes had reached fixation, unfitness based selective loss of Neanderthal genes that had negative functionality relative to modern human variants, and loss of selectively neutral Neanderthal genes due to random genetic drift experienced in serial founder effects particularly at population bottleneck moments for West Eurasians and East Eurasians respectively. 

11.  The fact that the specific Neanderthal genes found in West Eurasian and East Eurasian populations differ materially from each other also supports a conclusion that the population genetic isolation of West Eurasians from East Eurasians during the Paleolithic era was almost complete.

12.  A small subset of Neanderthal admixed genes are found in modern human populations at frequencies that strongly suggest some sort of fitness enhancing selective effect that have caused them to be present at frequencies not consistent with selectively neutral random chance in their inheritance.

13.  No modern human men have Y-DNA haplogroups attributable to Neanderthals or any archaic hominins (of course, Y-DNA is uniparentally inherited patrilineally).   All modern human men with recent origins outside of Africa have Y-DNA haplogroups have root in either the most recent common ancestor of macro-haplogroup DE, or the most recent common ancestor of Y-DNA macro-haplogroup CF.  Both of these Y-DNA macro-haplogroups are rooted in a single modern human lineage, of which Y-DNA haplogroups A and B, which are private to Africa, are more basal.

14.  No modern humans have mtDNA haplogroups (a matrilineally inherited uniparental genetic marker) attributable to Neanderthals or any archaic hominins.  All modern human men with recent origins outside of Africa have mtDNA haplogroups have root in mtDNA haplogroup M or mtDNA haplogroup N, both of which are offshoots of mtDNA haplogroup L3.  The roots of mtDNA haplogroup L3 are African.  The roots of both mtDNA haplogroup L3 and all other mtDNA sub-haplogroups of mtDNA haplogroup L, many of which are more basal than the root of the L3 haplogroup, arise from a single mtDNA most recent common ancestor ("mitchondrial eve"), and all or almost all of the sub-haplogroups of mtDNA haplogroup L after private to Africa or predominantly African in their distribution.  While mtDNA subhaplogroup M1 is found in Africa (predominantly Northern and Eastern Africa), it is widely believed to have back migrated to Africa from Southwest Asia sometime long after the Out of Africa event, probably in the Upper Paleolithic era.  Other non-haplogroup L mtDNA haplogroups are believed to be more recent back migrations to Africa and are rare in non-Afro-Asiatic linguistic populations with a handful of exceptions near the Afro-Asiatic linguistic boundary or attributable to historic era migrations.

15.  There is no other genetic indication of archaic hominin admixture with modern humans outside Africa at this time.

16.  There are some indications from African autosomal genetics that there may have been archaic admixture, possibly two separate events in different places with different archaic hominin species as recently as 18,000 years ago, with the ancestors of relict hunter-gatherer populations in Africa, Southern African Khoisan peoples and Pygmy peoples.  Genetic evidence suggest that these "Paleoafrican" populations have the most basal break from other modern human populations in tree-like modern human genetic phylogenies.  The most recent common ancestor of other African populations, including the African populations from which all non-Africans are genetically derived, is more recent than the Paleoafrican branch's split from other Africans.  There is no evidence at this time of archaic hominin admixture (i.e. admixture with archaic hominin who has speciated from modern humans long before the species was established who were not directly ancestral to modern humans) with the ancestors of African populations other than Paleoafricans that is not derivative of Eurasian Neanderthal admixture.  

Modern Humans Arrive In India and Expand Into The Rest Of Asia From There.

17.  There were modern humans in India before there were modern humans in Europe.

18.  The earliest dates suggested for modern humans remains in Asia to the east of India come from around 100,000 years ago in Southern China, although their classification as archaic v. modern human is hotly disputed, the finds are outliers, and the dates are subject to question due to their outlier status and major corrections to other Asian archaeological dates in the last half century.  Likewise the latest widely accepted dates for archaic, non-Neanderthal hominins in Asia to the south of Siberia and to the east of Pakistan are about 100,000 years ago.

19.  The latest possible date for modern humans in Asia is 45,000 years ago, when there is definitive Papuan and Australian evidence, plus at least a few thousand years from migration from India to Papua New Guinea and Australia.  The archaeological record is too thin to support any particular date of modern human arrival in Asia beyond India in the time period from 45,000 to 100,000 years ago, and the mutation rate based genetic estimates are not definitive enough to clearly resolve the question.

20.  The extent to which lithic technological cultures can be definitively associated with particular hominin species is hotly disputed and distinguishing between stone tools found in sites where they are definitively associated with modern humans in the Mesolithic (i.e. basically after modern humans evolve, but before modern humans arrive in Europe) from stone tools found in sites that are definitively associated with Neanderthals, without the remains to guide that determination, is a subtle art.  Only in subsequent Upper Paloelithic era do the distinctions between modern human tool artifacts and Neanderthal artifacts become more obvious.  In earlier periods when modern humans coexisted with Neanderthals in the Levant, the distinctions are far less clear.

21.  Similarly, while there are clear distinctions between more primative Asian archaic hominin stone tools first used by Homo Erectus and the first distinctive, pre-modern human era stone tools of Neanderthals in Europe, the extent to which different tool technologiess strictly correspond to a Homo Erectus v. Neanderthal species distinction in liminal areas like South Asia, when not found in association with hominin remains, is hotly disputed.

22.  The modern humans who initially arrived in Southeast Asia, Indonesia, Papua New Guinea, Australia, East Asia, Tibet, Oceania and Japan were all descendants of modern humans who traversed India (i.e. they arrived via a "Southern route").  It follows, of course, that there were modern humans in India before there were modern humans in any of these other places.  The modern humans who first peopled all these places with modern humans did not have ancestors who made their way into Asia from Europe or Central Asia or Siberia.  The population genetic evidence to support this proposition from Y-DNA, mtDNA, the details of Neanderthal admixture, Denisovian admixture, and autosomal genetics is overwhelming and consistent on this point. 

23.  The Toba volcanic erruption, the largest in the pre-historic out of Africa era, took place approximately 75,000 years ago in Indonesia.  The direct effects of the Toba erruption (e.g. notable deposits of ash) ranged mostly from the Toba volcano in Indonesia to India (with magma itself probably only affecting the unfortunate residents of the island itself).  What are currently the jungles of Burma would have been particularly hard hit.

24.  It isn't entirely clear what kind of global climatic impact the erruption may have had.  The most recent climate models have tended to downplay the extent to which the Toba erruption could have wiped out modern humans in the Levant (in a failed out of Africa scenario) or wiped out Homo Erectus in Asia very far to the east of the volcano.  The Toba erruption roughly coincides with the beginning MIS 4, the cooler Paleoclimate period following the interglacial in MIS 5.

25.  There were probably modern humans in India both before and after the Toba erruption as indicated by lithic tools on both sides of deposits of Toba ash there that are in continuity with later confirmed modern human populations there.

26.  The biogeographic Wallace Line that has mainland Southeast Asia and most of Southeast Asia and the Phillipines on one side, and Papua New Guinea and Australia on the other, has never been crossed by a land bridge at any time that hominins have been present outside of Africa (i.e. in the last two million years).

27.  Papuans and aboriginal Australians have autosomal genetic profile that show substantial admixture (about 8%), in additional to older East Eurasian typical Neanderthal admixture of about 2.5%, with archaic hominins substantially similar to ancient DNA extracted from bones in a Siberian cave at Denisovia.  There may have some independent traces of Denisovian admixture in Phillipino negrito populations, but all other Denisovian admixture in the world is traceable to these sources.

28.  The arrival of modern humans in Australia triggered by some means a mass megafauna extinction there, and took place at a time when Papua New Guinea, Australia and Tasmania were a single continental mass.  Modern humans were present in Papua New Guinea and Australia around 45,000 years ago and not too many thousands of years before then.

29.  The arrival of modern humans in Australia and Papua New Guinea, as I understand it, took place at a time when Indonesia up to the Wallace line has not yet been connected to mainland Asia as it was during the last glacial maximum when sea levels were lower.  Indonesia was (and the Philippines were), as it is today, an island chain divided by shallow water ocean straights around 45,000 years ago.

30.  It is not clear if there were land bridge moments in Indonesia after the arrival of Homo Erectus ca. 1,900,000 years ago (Java man) and before the Last Glacial maximum, although it doesn't seem unreasonable to think that there might have been such time periods.

31. Homo Florensis appears to have been in Flores from ca. 100,000 years ago until about 18,000 years ago and to have co-existed with modern humans for tens of thousands of years on the island with is on Australia's side of the Wallace line.

32. The population genetics of Asia indicate that the Paleolithic demographic history of the region is probably more complex than a single wave of pre-Neolithic migration, and is complicated by major impacts from Neolithic era migrations.

33. Modern humans arrived in Japan around 30,000 year ago and in Tibet sometime before the last glacial maximum.

34. There was a megafauna extinction in Siberia around 30,000 years ago.

Modern Humans Arrive In Europe and the Americas, Archaic Hominins Go Extinct

35.  Modern human migrated to Europe around 45,000 years ago, give or take a few thousand years and were found throughout Europe within a few thousand years.

36.  The arrival of modern humans in Europe coincided with a period of major volcanic erruptions in Southern Europe and at least some period of volcanic ash induced climatic cooling.

37.  Neanderthals and Siberian Denisovians were extinct by about 28,000 years ago, well before the Last Glacial maximum and well before the founding population of the Americas in Beringia was established.

38.  The last glacial maximum was about 20,000 years ago.  Most of Northern Europe and Siberiia was underneat glaciers at this point in time. Sea levels were lower then than at another other time in the Out of Africa era giving rise to the Berginian land bridge and the connected Sahul land mass.

39. After modern humans arrived in Australia, ocean straights divided Papua New Guinea and Tasmania from its land mass.

40. After Tasmania became separated from Australia, a small number of dingos were introduced in Australia from Southeast Asia (presumably via Indonesia) and this triggered a secondary wave of marsupial animal extinction in Australia.

41. Homo Florensis (in Flores, Indonesia) and any archaic hominin species in Africa were extinct by about 18,000 years ago, leaving modern humans as the sole surviving species of hominins on Earth.

42. The founding hominin population of the Americas consisted entirely of modern humans who (with the possible exception of a handful of individual on the Atlantic side of the continent divide who had no material long term demographic or ecological impact) arrived there via a Beringian land bridge within plus or minus a few thousand years of the Last Glacial Maximum, and made their way into the rest of North America and South America sometime within a few thousand years after the Last Glacial Maximum. It took no more than a few thousand years once this passage has opened for modern humans to make it from Beringia to the farthest point in South America. The arrival of modern humans in the Americas triggered, by some means, a mass megafauna extinction in the Americas.

43. The founding modern human population of the Americas predominantly derive from peoples who ancestestors made their way to Beringia via the Southern route through India, although there may have been a minor component of the founding population of the Americans (exemplified in the mtDNA haplogroup X found in indigeneous Americans) that made its way to Beringia instead from Southwest Asia via a Northern route through Siberia.  It isn't entirely clear if this Northern route component was part of the initial founding population wave of a later wave of migration into the Americas.

44.  There are substantial population isolation genetically between South American and North American populations in the pre-Columbian era.

45.  The sudden cooling period of the Younger Dryas, following a post-last glacial maximum warming period, was triggered by an extraterrestrial impact about 16,000 years ago.  We are now in an interglacial climate period known of the Holocene which started around 10,000 years ago.

46.  There appear to have been major population migrations in the time period after the last glacial maximum and before the Neolithic revolution in the Mediterranean basin, as well as a repopulation of Northern Eurasian latitudes.

47.  The Na-Dene peoples of North America derive genetically, in part, at least, from a wave of migration sometime after the founding population of North America and sometime before the Inuit people arrived.  The Na-Dene migrated to the American Southwest around 1000 years ago.

48.  The modern Inuit population of North America derives in substantial part from Siberian ancestors who were not part of the founding population of North America and instead arrived as part of the Thule migration wave, an archaeologically well dated migration wave after the Dorset people, during the historic era (although pre-Columbian).

49.  A historically attested and archaelogically confirmed group of Vikings with roots in Europe associated with Lief Erikson arrived in North America about 1000 years ago in coastal Canada, but the colony quickly collapsed, had no major genetic or ecological impact on North America, and is not clearly attested in any surviving indignenous American folklore.

50.  The arrival of Europeans in the Americans with Columbus in 1492 had dramatic effects, mostly on the Americas but also on the rest of the world due to impact flow from the Americas.

Thursday, July 5, 2012

Population Genetics Quick Hits

Excerpts from abstracts of papers to be presented at aa population genetics conference this summer here and here via Dienekes' Anthropology blog:

Wheat domestication:

The past 15 years have witnessed a notable scientific interest in the topic of crop domestication and the emergence of agriculture in the Near East. . . . some seemingly conflicting evidence, especially in the case of emmer wheat, caused certain controversy and a broad scientific consensus on the circumstances of the wheat domestication has not been reached. . . . the main cause of the above mentioned inconsistencies might lie in the inadequacy of the divergent, tree-like evolutional model. The inconsistent phylogenetic results and implicit archaeological evidence indicate a reticulate (rather than divergent) origin of domesticated emmer. Reticulated genealogy cannot be properly represented on a phylogenetic tree. . . . On a genome-wide super-tree, the conflicting phylogenetic signals are suppressed and the origin of domesticated crop may appear monophyletic, leading to misinterpretations of the circumstances of the Neolithic transition. The network analysis of multi-locus sequence data available for tetraploid wheat clearly supports the reticulated origin of domesticated emmer and durum wheat.

In other words, when hybrids are involved, phylogenetic trees start to look like Ewok villages.

Global population genetics:

There has been recent excitement and debate about the details of human demographic history, involving gene flow that has occurred between populations as well as the extent and timing of bottlenecks and periods of population growth. Much of the debate concerns the timing of past admixture events; for example, whether Neanderthals exchanged genetic material with the ancestors of non-Africans before before or after they left Africa. . . . [W]ithin the populations sequenced by the 1000 Genomes consortium, we find evidence that there was no significant gene flow between Europeans and Asians within the past few hundred generations. It also looks unlikely that the Yorubans of Nigeria interbred with Europeans or Asians in a population-specific way, though there may have been admixture between [some] Africans and an ancestral non-African population.

Put another way, the genetic exchanges between Africa and Europe probably post-date the non-Paleoafrican West African founding population and did not extend as far as West Africa (or Southern Africa) until the European colonial era. These empirical results, taken together with statistical models that show that even very slight gene flow can dramatically link large populations surprisingly quickly, suggest that the level of regional population isolation until very recently was very extreme.


We applied our method to polymorphism data in European and East Asian individuals from the 1000 genomes project, in conjunction with the draft sequence of the Neandertal genome, to obtain the first genomewide map of Neandertal ancestry. Analysis of this map reveals several findings: 1. We identify around 35,000 Neandertal-derived alleles in Europeans and 21,000 in East Asians. 2. The map allows us to identify Neandertal alleles that have been the target of selection since introgression. We identified over 100 regions in which the frequency of Neandertal ancestry is extremely unlikely under a model of neutral evolution. The highest frequency region on chromosome 4 has a frequency of Neandertal ancestry of about 85% in Europe and overlaps CLOCK, a key gene in Circadian function in mammals. The high frequency, Neandertal-derived variant is specific to Europeans; it is not very common in East Asians. This gene has been found in other selection scans in Eurasian populations, but has never before been linked to Neandertal gene flow. 3. Several of the Neandertal-derived alleles identified in 1) above are found in the >6,000 SNPs associated with common diseases listed in the NHGRI catalog. These Neandertal derived variants are found to be risk variants associated with obesity and protective variants against breast cancer. 4. We also investigate the possibility of using this map to reconstruct the genome of the introgressing Neandertal. Using the ancestries in Europe and East Asia, we can reconstruct about 600 Mb which we expect to increase with larger samples and additional populations.

The West Eurasian v. East Eurasian differences in Neanderthal admixture must have occured separately but comparably in West Eurasians and East Eurasian founding populations (both not long after that basic West-East split of the respective founding populations), or must have resulted from a pretty complete fission of a Eurasian founding population at a time when genes introgressed from Neanderthals had not yet reached fixation on the original Out of Africa population.

Either way, the West Eurasian v. East Eurasian split in the Out of Africa population has to come very early, and the notion of a many millenia long Eurasian Eden period prior to this split and after Neanderthal admixture is disfavored. In an unstructured population of tens of thousands of people, which is approximately the size of the Eurasian founding population on a census basis, which probably did not exceed a few hundred thousand for many millenia, it would have taken only a dozen or few generations (a few centuries) for the West Eurasian and East Eurasian components of Neanderthal admixture to be much more similar than they are in reality.

Any extended Eurasian Eden period, during which non-Africans grew genetically distinct from Africans before splitting into West Eurasian and East Eurasian branches, would have had to have taken place before any significant Neanderthal admixture in that population.

The earliest archaeological evidence for modern humans outside Africa, which is more than 100,000 years ago, and even the earliest evidence of continuous modern human presence of modern humans outside Africa, which is more than 75,000 years ago, far precedes the arrival of modern humans in Europe (ca. 40,000 years ago) or Neanderthal extinction (ca. 29,000 years ago). Both the 100,000 year ago evidence from the Levant and the 75,000 year ago evidence from the Levant suggests that modern humans were contemporaneous with Neanderthals there at these times (with a possible absence of more than twenty-millenia in between these time periods).


A draft genome sequence was determined in 2010 from a small finger bone found in Denisova Cave in southern Siberia and was recently completed to 30-fold coverage. Its analysis reveals that it derived from an individual that belonged to a population related to, but distinct from, Neandertals. A large molar has also been described from Denisova Cave and shown to carry an mtDNA genome closely related to that of the finger bone.

A second molar was found in Denisova Cave in 2010. We have captured and sequenced the complete mitochondrial genome of this tooth. While the mtDNAs of the finger bone and the first molar differ at only two nucleotide positions, they carry 86 and 84 differences, respectively, to the second molar. Thus, the maximum amount of mtDNA differences observed among these three Denisovans found within one cave is almost twice as large as the maximum differences seen among six Neandertals for which complete mtDNAs are available. Interestingly, the mtDNA of the second molar has a shorter branch than the other two Denisovan mtDNAs, suggesting that it may be older than the others.
If, as I suspect, Denisovians have a significant Asian Homo Erectus descent, then we would expect more genetic diversity in their nearly two million year old Out of Africa lineage than in Neanderthals whose emergence is not more than about six hundred thousand years old and perhaps considerably more recent than that date.

Paleoafrican genetics:

[W]e sequenced the whole genomes of five individuals in each of three geographically and linguistically diverse African hunter-gatherer populations. . . . In these 15 genomes we identify 13.4 million variants, many of which are novel, substantially increasing the set of known human variation. These variants result in allele frequency distributions that are free of SNP ascertainment bias. This genetic data is used to infer population divergence times and demographic history (including population bottlenecks and inbreeding). . . . These highly-divergent genomic regions include genes involved in immunity, metabolism, olfactory and taste perception, reproduction, and wound healing.


Previous studies have shown an ancient divergence (~60,000 years ago) of the ancestors of modern day Pygmies from non-Pygmies, and a more recent split of the Eastern and Western Pygmy groups. . . . we sequenced the [whole] genomes of 47 individuals from three populations: 20 Baka, a Pygmy hunter-gatherer population from the Western subgroup of the African Pygmies; 20 Nzebi, a neighboring non-Pygmy agriculturist population from the Bantu ethnolinguistic group; as well as 7 Mbuti, Eastern Pygmy population, from the Human Genome Diversity Project (HGDP). . . . we call over 17 Million SNPs across the three populations, 32% of them novel. . . . Preliminary results show relatively low genetic differentiation between the Baka and the Nzebi (mean FST = 0.026), whereas the Mbuti show higher differentiation to both Baka and Nzebi (mean FST = 0.060 and 0.070, respectively).


The San and Khoe people currently represent remnant groups of a much larger and widely distributed population of hunter-gatherers and pastoralists who had exclusive occupation of southern Africa before the arrival of Bantu-speaking groups in the past 1,200 years and sea-borne immigrants within the last 350 years. Mitochondrial DNA, Y-chromosome and autosomal studies conducted on a few San groups revealed that they harbour some of the most divergent lineages found in living peoples throughout the world. . . . we successfully genotyped . . . 220 individuals, comprising seven Khoe-San, two Coloured and two Bantu-speaking groups from southern Africa. . . .

We found that six of the seven Khoe-San populations form a common population lineage basal to all other modern human populations. The studied Khoe-San populations are genetically distinct, with diverse histories of gene flow with surrounding populations. A clear geographic structuring among Khoe-San groups was observed, the northern and southern Khoe-San groups were most distinct from each other with the central Khoe-San group being intermediate. The Khwe group contained variation that distinguished it from other Khoe-San groups. Population divergence within the Khoe-San group is approximately 1/3 as ancient as the divergence of the Khoe-San as a whole to other human populations (on the same order as the time of divergence between West Africans and Eurasians). Genetic diversity in some, but not all, Khoe-San populations is among the highest worldwide, but it is influenced by recent admixture. We furthermore find evidence of a Nilo-Saharan ancestral component in certain Khoe-San groups, possibly related to the introduction of pastoralism to southern Africa.

The latest information on Paleoafrican genetics refines, but largely confirms the status quo pre-history of Africa. Genetic data suggest that African hunter-gatherer populations diverged from other Africans at roughly the same time as indicated by mutation and recombination rates as the Out of Africa event, and at the very least, in the Mesolithic era prior to modern human presence in Europe, Australia, Papua New Guinea, Japan, Tibet, or the Americas. These small populations have many genetic variations found nowhere else, some of which are probably basal and provide unique insights into early modern human genetics, and others of which probably reflect selective evolution for their circumstances as hunter-gatherers in marginal territories. Their Bantu and European and Asian ancestries, when observed, are well understood in the historic context of colonialism, and the near pre-historic context of Bantu expansion.

These studies reinforce the notion that these populations have highly substructured population genetics, rather than being drawn from a homogeneous Paleoafrican population. This contrasts sharply with population like those of indigeneous North and South Americans, indigneous Papuan and Australian populations, Jomon Japan, the Andaman Islands, and Arctic Finland's Saami population (one of Europe's last populations to transition from hunting and gathering to pastoralism), whose population genetics are all show characteristic signs of being derived from small founding populations that placed a bottleneck on subsequent genetic diversity. Indeed, non-African population genetics, in general, show a derivation from a relatively modest sized founding population.

The evidence of a Nilo-Saharan ancestral component in certain Khoe-San groups is also new.

West African genetics:

The Niger-Congo phylum encompasses more than 1500 languages spread over sub-Saharan Africa. This current wide range is mostly due to the spread of Bantu-speaking people across sub-equatorial regions in the last 4000-5000 years. Although several genetic studies have focused on the evolutionary history of Bantu-speaking groups, much less effort has been put into the relationship between Bantu and non-Bantu Niger-Congo groups. Additionally, archaeological and linguistic evidence suggest that the spread of these populations occurred in distinct directions from the core region located in what is now the border between Nigeria and Cameroon towards West and South Africa, respectively. We have performed coalescent simulations . . . in order to statistically evaluate the relative probability of alternative models of the spread of Niger-Congo speakers and to infer demographic parameters underlying these important migration events.

We have analysed 61 high-quality microsatellite markers, genotyped in 130 individuals from three Bantu and three non Bantu-speaking populations, representing a "Southern wave" or the Bantu expansion, and a "Western wave", respectively. Preliminary results suggest that models inspired by a spatial spread of the populations are better supported than classical isolation with migration (IM) models. We also find that Niger-Congo populations currently maintain high levels of gene flow with their neighbours, and that they expanded from a single source between 200 and 600 generations[.]

I would quarrel with the claim that the lingustic evidence supports a non-Bantu expansion was centered at a place more or less identical to the Bantu expansion. The Niger-Congo expansion is widely viewed in linguistic circles as happening earlier than Bantu expansion from a location to the North of this location. The archaeological record is thin, any way you cut it.

A Niger-Congo expansion time of 200 to 600 generations sounds more precise than it seems - this covers a period from about 18,000 years ago to the eve of Bantu expansion, depending on the demographic parameters applied. All this shows is that Niger-Congo expansion did not happen in the early Upper Paleolithic, which the reasonable coherence of most of the Niger-Congo language family has always suggested was probably the case.

Mediterranean genetics:

We identify a complex pattern of autochthonous, European, Near Eastern, and sub-Saharan components in extant North African populations; where the autochthonous component diverged from the European and Near Eastern component more than 12,000 years ago, pointing to a pre-Neolithic ‘‘back-to-Africa’’ gene flow.

To estimate the time of migration from sub-Saharan populations into North Africa, we implement a maximum likelihood dating method based on the frequency and length distribution of migrant tracts, which has suggested a migration of western African origin into Morocco ~1,200 years ago and a migration of individuals with Nilotic ancestry into Egypt ~ 750 years ago.

We characterize broad patterns of recent gene flow between Europe and Africa, with a gradient of recent African ancestry that is highest in southwestern Europe and decreases in northern latitudes. The elevated shared African ancestry in SW Europe (up to 20% of the individuals’ genomes) can be traced to populations in the North African Maghreb. Our results, based on both allele-frequencies and shared haplotypes, demonstrate that recent migrations from North Africa substantially contribute to the higher genetic diversity in southwestern Europe.

Central Asian genetics:

[W]e focus on human populations in Central Asia, a region that has long been known to contain the highest genetic diversity on the Eurasian continent. However, whether this variation principally reflects long-term presence, or rather the result of admixture associated with repeated migrations into this region in more recent historical times, remains unclear. Here we investigate the underlying demographic history of Central Asian populations in explicit relation to Western Europe, Eastern Asia and the Middle East. . . . we find that present patterns of genetic diversity in Central Asia may be best explained by a demographic history which combines long-term presence of some ethnic groups (Indo-Iranians) with a more recent admixed origin of other groups (Turco-Mongols). Interestingly, the results also provide indications that this region might have genetically influenced Western European populations, rather than vice versa.


Kyrgyzstan . . . we focused on two populations in Central Asia with long-term contrasted lifestyles: Kyrgyz’s that are traditionally nomadic herders, with a traditional diet based on meat and milk products, and Tajiks that are traditionally agriculturalists, with a traditional diet based mostly on cereals. . . . Tajiks display a much larger proportion of common ancestry with European populations while Kirgiz’s share a larger common ancestry with Asiatic populations.
South Asian genetics:

Linguistic and genetic studies have demonstrated that almost all groups in South Asia today descend from a mixture of two highly divergent populations: Ancestral North Indians (ANI) related to Central Asians, Middle Easterners and Europeans, and Ancestral South Indians (ASI) not related to any populations outside the Indian subcontinent. ANI and ASI have been estimated to have diverged from a common ancestor as much as 60,000 years ago, but the date of the ANI-ASI mixture is unknown.

Here we analyze data from about 60 South Asian groups to estimate that major ANI-ASI mixture occurred 1,200-4,000 years ago. Some mixture may also be older—beyond the time we can query using admixture linkage disequilibrium—since it is universal throughout the subcontinent: present in every group speaking Indo-European or Dravidian languages, in all caste levels, and in primitive tribes. After the ANI-ASI mixture that occurred within the last four thousand years, a cultural shift led to widespread endogamy, decreasing the rate of additional mixture.


Human skin colour is a polygenic trait that is primarily determined by the amount and type of melanin produced in the skin. The pigmentation variation between human populations across the world is highly correlated with geographic latitude and the amount of UV radiation. Association studies together with research involving different model organisms and coat colour variation have largely contributed to the identification of more than 378 pigmentation candidate genes. These include TYR OCA2, that are known to cause albinism, MC1R responsible for the red hair phenotype, and genes such as MATP, SLC24A5 and ASIP that are involved in normal pigmentation variation. In particular, SLC24A5 has been shown to explain one third of the pigmentation difference between Europeans and Africans. However, the same gene cannot explain the lighter East Asian phenotype; therefore, light pigmentation could be the result of convergent evolution.

A study on UK residents of Pakistani, Indian and Bangladeshi descent found significant association of SLC24A5, SLC45A2 and TYR genes with skin colour. . . . We have tested 15 candidate SNPs for association with melanin index in a large sample of 1300 individuals, from three related castes native to South India. Using logistic regression model we found that SLC24A5 functional SNP, rs1426654, is strongly associated with pigmentation in our sample and explains alone more than half of the skin colour difference between the light and the dark group of individuals. Conversely, the other tested SNPs fail to show any significance; this strongly argues in favour of one gene having a major effect on skin pigmentation within ethnic groups of South India, with other genes having small additional effects on this trait. We genotyped the SLC24A5 variant in over 40 populations across India and found that latitudinal differences alone cannot explain its frequency patterns in the subcontinent.
The proposed ANI-ASI admixture date is not inconsistent with a proposed time frame for an Indo-Aryan migration into India, although it is suspiciously young and may conceal pre-existing ANI-ASI divisions due to inadequacies of the model.

South Asian skin coloration turns out to be genetically quite straight forward and to involve the same gene that is most important in distinguishing Europeans and Africans from each other in skin color. The fact that the same genetics are not at work in East Asians and do not correlate well with latitude in South Asia suggest that these skin color differences arose after the initial waves of Southern route migration into Asia and that they have a significant Holocene admixture as opposed to evolutionary selection source.

European genetics:

About 11,000 years ago, a change in human lifestyle took place in the territories of present-day western Iran, the Levant region and south-east Anatolia, which is characterised particularly by four factors: the people founded permanent settlements with buildings for various functions; plants such as Einkorn and beans were cultivated; goats, sheep, pigs and cattle were domesticated; a new kind of culture evolved, that became conspicuous with the appearance of a new material culture including ground stone tools and later, pottery products. The transition from the partly nomadic hunter-gatherer subsistence strategy to a settled lifestyle based on food production is also known as the “Neolithic Revolution”. About 8,500 years ago, the Neolithic culture spread to the southeast of Europe and later expanded episodically across central and northern Europe. The extent to which this movement of a farming culture was accompanied by a movement of people, as opposed to just a spread of ideas and skills, has been a subject of considerable debate and dispute over the last 100 years.

Population genetic computer simulations of genetic data from ancient human remains, based on coalescent theory have shown that the early Neolithic farmers could not have been descended just from the later hunter-gatherers of central Europe (Bramanti et al. 2009). As the hunter-gatherers had already been settled in Central Europe since the retreat of the glaciers 20 kya, Neolithic famers must have migrated into this area.

There is good evidence of cultural contact between hunter-gatherers and early farmers in central Europe. Whether the exchange of hunting tools also led also to the exchange of men is still not clear, as Y-chromosomal DNA has not yet been studied systematically in ancient human remains. Moreover, ancient DNA evidence is now emerging that other regions don't follow the patterns of population discontinuity observed in Central Europe. While the overall results support a model of demic diffusion of farmers from southeastern Europe, or even further East, into Central Europe, it is very likely that modern populations in most parts of Europe were formed by varying degrees of admixture between incoming farmers and indigenous hunter-gatherers.


The Etruscan culture is documented in Etruria, Central Italy, from the 7 th to the 1 st century BC. For more than 2,000 years there has been disagreement on the Etruscans’ biological origins, whether local or in Anatolia. Genetic affinities with both Tuscan and Anatolian populations have been reported, but so far all attempts have failed to fit the Etruscans’ and modern populations in the same genealogy. We extracted and typed mitochondrial DNA of 14 individuals buried in two Etruscan necropoleis, analyzing them along with other Etruscan and Medieval samples, and 4,910 contemporary individuals. Comparing ancient and modern diversity with the results of millions of computer simulations, we show that the Etruscans can be considered ancestral, with a high degree of confidence, to the modern inhabitants of two communities, Casentino and Volterra, but not to most contemporary populations dwelling in the former Etruscan homeland. We also estimate that the genetic links between Tuscany and Anatolia date back to at least 5,000 years ago, strongly suggesting that the Etruscan culture developed locally, without a significant contribution of recent Anatolian immigrants.

This result tends to disfavor a priori the likelihood that the Etruscan and Rhaetic languages were part of the same linguistic family as pre-Indo-European Aegean languages that have been previously linked to them based on some rather thin evidence. This abstract doesn't shed much light on whether the Roman era Rhaetic Swiss from whom the Etruscans are historically attributed to have been linked ethnically and linguistically were themselves, was a refugium population displaced from Gaul by Celtic peoples. But, it does confirm that Etruscans were demically replaced in most of Tuscanny, as earlier ancient DNA studies had suggested. Earlier studies had left open the possibility that the Etruscans had been genocidally extinguished entirely by the Romans, but it now looks as if this did not happen.

Indigenous Puerto Ricans:

[T]he ancestry-specific PCA plotted the Puerto Rican Native segments tightly clustered with the Native segments of groups from the same language family as the Tainos (Equatorial-Tucanoan), showing a clear association between linguistics and genetics instead of a geographical one.
The nature of Puerto Rican indigeneous ancestry has been controversial. This finding supports the conclusion that the indigeneous ancestry of Puerto Ricans is indeed local to the island and can be traced back to the era of Columbian first contact, rather than constituting hodge podge of indigeneous roots from across the Americans that arrived via colonial era trade routes.

Higgs Discovery Confirmed And Close To SM

In a triumph for theoretical physicists who predicted its existence in 1964, both ATLAS and CMS (the two Large Hadron Collider experiments) have independently confirmed at the five standard deviation threshold that is customarily viewed as the threshold for a discovery in high energy physics, a new particle that is almost certainly some form of Higgs boson. Tevatron announced indications of the existence of a Higgs boson at 2.9 standard deviation significance level in the dominant Higgs boson decay mode to a pair of bottom quarks earlier this week.

According to the best estimates of CMS the "Mass of Higgs is 125.3 += 0.6 GeV", while according to the best estimates of the ATLAS experiment the mass of the Higgs is 126.5 GeV and should have a similar margin of error. These estimates suggest that a Higgs boson weighs about as much as an atom with a combined 133 protons and neutrons, close to the mass of an iodine atom (but has a very short half-life). The Tevatron result estimates the Higgs boson mass to only about +/- 10GeV to 15 GeV, but is not inconsistent with the LHC estimates of the Higgs boson mass.

The statistical significance of combined Higgs boson data

The combined data from all the experiments indicates that a Higgs boson exists at a considerably higher level of significance.

The data is reported by statistical significance in each decay channel. For the combined data the significance level, computed using some shortcuts from a truly accurate combination that have proved to be immaterial when the final analysis is done is as follows (the term "sigma" used in the quoted material is the term used in high energy physics for standard deviations of statistical significance):

The combined diphoton plot gives a 6 sigma signal. It is 2.4 sigma stronger than the standard model. . . . for ZZ to four leptons. Significance is an impressive 4.6 sigma . . . in this channel it matches perfectly the standard model Higgs. . . . the two low resolution channels across ATLAS+CMS [diphoton+ZZ] . . . gives [a] 7.4 sigma [signal]. . . we have now eliminated any possibility of a second boson nearby, unless they are too close to separate.

Put all of the data together and you get a combined statistical significance of 7.45 standard deviations for the existence of a Higgs boson of a mass of approximately 125.5 GeV (note that the date in the image below reflects the European convention and would read 7/4/2012 in the American numerical date order convention).

Is it the Standard Model Higgs boson?

As the pre-eminent Higgs blogger in the world (whose blog is the source of all of the links in this post) explains, the data, taken together, probably support the a priori favored result that the particle that has been discovered is a Standard Model Higgs boson with all of its properties, although an unexpectedly high number of diphoton channel decays leaves open the possibility that we may also be seeing some beyond the Standard Model physics as well.

Is it the Higgs? . . .

The facts are that the boson discovered with a mass of about 125 GeV or 126 GeV interacts with a wide range of particles in exactly the way the Higgs boson should. Its decay modes to Z, W, b and tau have just the right ratios and its production has also been tested in different ways confirming indirectly that its coupling to the top quark is also about right. Its spin could be 0 or 2 but 0 is much more likely. All these features point to the standard model Higgs boson.

The only fly in the ointment is its decay rate to two photons. This is nearly twice as large as expected. The significance of the discrepancy with the standard model is about 2.5 sigma.

It could be a fluke.
We have learnt to show some healthy skepticism when it comes to observations of physics beyond the standard model. However it is also consistent with an enhancement due to the presence of another charged boson. If that boson exists it must have a mass at least a bit larger than the W otherwise the Higgs would decay to this particle in pairs and we would see the effect on the other decay rates. It can’t be too massive otherwise it would not enhance the diphoton rate enough. But it is likely to be possible to find a range of masses and properties that is consistent with all the observations.

So it is not necessary to invoke any properties for the observed boson that are any different from the standard model. Separate new physics will suffice. So the observed boson passes several tests required by the Higgs and I think that it is reasonable to assume that is indeed the Higgs boson until some observation suggests otherwise.

It is worth noting that the diphoton channel was the primary means by which scientists at the LHC determined that there was a Higgs boson at all (because it is such a "clean" channel that is relatively free of "background" events from other processes), so a Higgs boson discovery at an arbitrary five sigma level is more likely to take place during a run where random statistical variation produces an above average, rather than a below average or average number of diphoton events.

Also, the raw number of diphoton events isn't particularly great. The diphoton channel is a quite uncommon form of Higgs boson decay, even though it a very clean Higgs boson detection channel since almost nothing else but Higgs boson decays produce diphoton channel decays, while almost all higher frequency Higgs boson decay results can also be produced by other decaying particles whose background frequency must be statistically separated from the Higgs boson sourced events. The most common Higgs boson decay channel is actually the bottom quark-anti-bottom quark channel, but the LHC actually has a harder time identifying Higgs boson source events than Tevatron, because the LHC's higher event energies produce such much background noise in that decay channel.

Flukes in rare events happen. Notwithstanding the fact that Gaussian estimates of statistical sampling variation should capture this tendency and reflect it in the sigma levels of low frequency events, the lessons of experience have taught physicists the conventional wisdom that even three sigma events turn out to be statistical flukes about half of the time. Put another way, the sigmas that physicists calculate are roughly twice as large as their real life experiences would suggest that they are, because somehow or other, there are systemic flaws in the way that they estimate error as a consequence of hard to accurately quantify factors like look elsewhere effects and systemic experimental errors.

So, a 2.5 sigma excess in the number of diphoton events observed when the Higgs boson is first detected is really much less exceptional that it would seem, especially given the considerations, both statistical and theoretical, that favor the a priori expectation that this is a Standard Model Higgs boson rather than a Beyond the Standard Model experimental result.

If we have seen a beyond the standard model diphoton result, rather than just a statistical fluke, the excess should fade in the next couple of years of LHC data. If this is an additional signal, however, the diphoton excess will be the dominant focus of beyond the standard model theoretical expectations at the LHC, since no other really notable beyond the standard model results, and certainly none with real statistical significance, have cropped up so far at the LHC.

Diphoton events are characteristically the product of even integer spin particle decays (i.e. spin zero or spin two), so it couldn't be experimental evidence of a new kind of quark or charged lepton. But, while the Standard Model predicts that there is just one Higgs boson, supersymmetry theories (SUSY) generically predict that there are multiple Higgs bosons, although different versions of those theories predict different numbers of them, with the most heavily discussed models featuring five rather than one Higgs boson, two of which typically have electrical charges. As Wikipedia explains:
The minimal Standard Model . . . contains only one complex isospin Higgs doublet, however, it also is possible to have an extended Higgs sector with additional doublets or triplets. The non-minimal Higgs sector favored by [beyond the standard model] theory are the two-Higgs-doublet models (2HDM), which predict the existence of a quintet of scalar particles: two CP-even neutral Higgs bosons h0 and H0, a CP-odd neutral Higgs boson A0, and two charged Higgs particles H±. The key method to distinguish different variations of the 2HDM models and the minimal SM involves their coupling and the branching ratios of the Higgs decays.

The so called Type-I model has one Higgs doublet coupling to up and down quarks, while the second doublet does not couple to quarks. This model has two interesting limits, in which the lightest Higgs doesn't couple to either fermions (fermiophobic) or gauge bosons (gauge-phobic). In the 2HDM of Type-II, one Higgs doublet only couples to up-type quarks, while the other only couples to down-type quarks.

Many extensions to the Standard Model, including supersymmetry (SUSY), often contain an extended Higgs sector. Many supersymmetric models predict that the lightest Higgs boson will have a mass only slightly above the current experimental limits, at around 120 GeV/c2 or less. The heavily researched Minimal Supersymmetric Standard Model (MSSM) belongs to the class of models with a Type-II two-Higgs-doublet sector and could be ruled out by the observation of a Higgs belonging to a Type-I 2HDM.

Thus, a sustained excess diphoton event signal would be the first really meaningful experimental evidence yet suggesting beyond the Standard Model particles seemingly similar to those predicted to exist in SUSY models. The quoted material on the diphoton excess above is obliquely alluding mostly to the possibility that we may be seeing the signal of charged Higgs particles H± within a pretty narrow mass range (more than 80 GeV but not all that much more than the Higgs boson that has just been discovered).

So, a disappearing diphoton event signal could essentially kill SUSY, while a sustained diphoton event signal could breath new life into SUSY and string theory.  Still, the absence of other replicated experimental evidence that is confirmed at LHC (e.g., the lack of excess top-antitop asymmetry, the non-detection of a lightest supersymmetric particle, the non-detection of neutrinoless double beta decay, the absence of vacuum instability given some fairly plausible assumptions about asymptotic safety in quatum gravity), leaves open the strong possibility that even if we are seeing the sign of a beyond the standard model particle in the excess diphoton decays, that we may not be seeing evidence of SUSY itself.

Of course, a sustained excess diphoton event signal could also point to something far less notable, like a subtle flaw in how the theoretically expected diphoton decay rate for Higgs bosons has been calculated, rather than anything as exciting as a newly discovered particle or force. Something as simple as a single sign error in the calculation that caused one Feynman diagram in a calculation to be doubled rather than cancelling out another diagram in the calculation could produce this discrepancy. A Higgs boson mass at the high end of the expected range could also reduce the magnitude of the discrepancy.

The clear discovery of a Higgs boson, however, clearly damages truly Higgsless models including technicolor, even if they leave some room for models with multiple Higgs bosons or composite Higgs bosons.

Coincidences associated with the current Higgs boson mass estimate

Crudely averaging the CMS and ATLAS mass results (arguably they should be weighted for their slightly different sample sizes) gives a result of 125.8 GeV +/- a one sigma amount of a bit less than 0.6 GeV.

This is not inconsistent with a previously observed possible empirical relationship between the Higgs boson mass and the mass of the W boson and Z boson that has no theoretical basis in the Standard Model itself: that the Higgs boson mass is approximately one half of the sum of twice the W boson mass plus the Z boson mass.

The currently estimated Higgs boson mass calculated with this formula used the best available W and Z boson mass estimates about 125.15 GeV, about 0.65 GeV off from the measured result, just a bit more than one sigma from the measured Higgs boson mass. In addition to uncertainty about the exact Higgs boson mass, there is some margin of error in the "theoretical prediction" of the formula due to the uncertainty in the masses of the W and Z boson mass used to estimate a 125.15 GeV mass from the formula. And, since there is a theoretically predicted relationship between the W and Z boson masses in the Standard Model via a "mixing angle constant" from the Standard Model, an error in one estimate of a weak force boson mass is not independent of an error in an estimate of the mass of the other weak force boson. There is a one sigma margin of error of something on the order of 0.2 GeV for this estimate from the uncertainty in the W and Z boson mass estimates. The combined uncertainties in the W boson, Z boson and Higgs boson mass estimates puts the experimental results within one sigma of each other.

The experimentally measured Higgs boson mass is probably inconsistent with a Higgs boson mass that is simply equal to one half of the vacuum expectation value of the Higgs field which would be 123 GeV.

All of these empirical formulas are complicated, however, by the fact that boson mass in the Standard Model "runs" with the energy level of the interaction according to a formula that is a function of the "beta functions" of the weak force and electromagnetic force coupling constants in the Standard Model. Particle masses are ordinarily stated at the coupling constant strength associated with the mass of the particular particle whose mass is reported, and when one is mixing the masses of multiple particles in a single equation it is arguably necessary to make some adjustments to the ordinary values of those masses to a common interaction energy level to be comparing apples to apples. These adjustment ought to be modest, since the Higgs boson is only a little more than 50% heavier than the W boson, the lightest of the particles in the formula. But, it isn't possible that after theoretically well motivated adjustments for the running of force coupling constants and particle masses with interaction energy levels that both the 2H=2W+Z and the 2H=Higgs vev formulas could be exactly correct. I'll leave the math and physics considerations regarding how these beta function adjustments could or should be applied to the physicists (at least for now).

Is the Higgs boson a quantum superposition of weak force bosons?

Notably, and this is merely my own speculation and I am sure, not an original one, a Higgs boson might be a quantum superposition of a the weak force bosons (the W+, W- and Z), rather than a fundamental particle. This is a theoretical approach that could produce such a simple mass formula for a Higgs boson along the lines of 2H=2W+Z in some manner, and has some Standard Model precedents.

We see something similar to this in the way that the eight rather than nine gluons that arise from different combinations of three color charges are described in the Standard Model, all of which have the same mass.

We also employ a similar mode of analysis to our understanding of a number of experimentally observed mesons (two quark composite particles) of the pseudoscalar (spin 0) and vector (spin-1) varieties. This include the neutral pi meson, the eta meson, the eta prime meson, the K-long meson and K-short meson (both of which are types of neutral kaons), the neutral rho meson, and the omega meson. All of these mesons are understood as linear combinations/quantum superpositions of different combinations of two or more pairs of charged quarks that have similar properties in some respect.

This kind of analysis could in principle suggest a way in which one could have anomalously high diphoton events consistent with a charged particle of the same mass making up some percentage component of the linear combination, in a manner similar to the way that the anomalous magnetic moment of a neutral composite particles like the neutron is generated which is much higher than it would be if it were a fundamental neutral particle rather than a composite one with charged quark components, without resorting to new fundamental particles not found outside the Standard Model. For example, this 2010 paper suggests that a composite Higgs boson model (perhaps based on a non-linear sigma model) could prduce an excess in a diphoton channel of production at LHC (see also here and here mentioning the similarity of non-linear sigma and "Little Higgs" models (e.g. reviewed here)).

This kind of linear combination/non-linear combination/quantum superposition analysis could kill both the Higgs boson mass coincidence and the diphoton event excess relative to the Standard Model in one stroke.

I'm probably wrong for reasons that I would understand if someone more knowledgable explained them to me, but the ansatz does present itself given what I do know.

The bottom line, at any rate, is that now that all of the constants of the Standard Model except the CP violation parameter for the lepton mixing matrix have at least somewhat meaningful experimental values, that it is now possible to engage in more serious consideration of potential deeper connections between the constants of the Standard Model than we have today, which could help point us towards some way to unify the three Standard Model forces and table of particles with a more fundamental theory. While a numerical coincidence does not prove a functional relationship between Standard Model constants, the more precisely know those constants are, the more plausible it is to think that empirical relationships between them have a deeper theoretical basis.

One more footnote

This result also continues the empirically perfect record the the humorous meta-theory of high energy physics that holds that fermions are always discovered in America, while bosons are always discovered in Europe.

UPDATE July 5, 2012: Slightly corrected to reflect comment.