Native American mtDNA

A recent blog post comprehensively summarizes the state of the art knowledge about which mtDNA haplogroups are Native American.

Uncontacted People

There are more than 7.4 billion people in the world. About 37,000 of them are in "uncontacted tribes" of which there are less than 200. Thus, all but 1 in 200,000 people on Earth have been contacted.

525 years ago, the population of the world was about 500 million, and the number of "uncontacted" people was on the order of 25 million or more. Thus, perhaps 1 in 20 people on Earth were "uncontacted." The proportion of the population that is uncontacted has fallen by a factor of 10,000 in the last 525 years (21 generations or less).

Ancient Pickling And Tanning Factories In Ireland?

The Old European culture blog has spent several posts examining various possible purposes of ancient structures, called fulachta fiadh found in Ireland that are basically wood lined basins in the ground, and has now hit upon a most plausible solution out of many of the proposals, which is that the structures served as facilities for pickling food and possibly also for tanning leather. 

There is one thing that I always wondered about fulachta fiadh: why were so many of them built in waterlogged acidic soil, near peat bogs? According to professor Aidan O'Sullivan "fulachta are often found in waterlogged soils by lakes, streams, fens, etc and often close to the edge of a bog. At Killoran fulachta were overwhelmingly located in glacial till at the edges of the bogs". 

Every single potential use of fulachta fiadh I have discussed so far would not have been possible if the fulacht fiadh trough was cut into a waterlogged acidic soil. Unless the trough was made absolutely watertight. Which most of them weren't. . . .

Any hole dug in an waterlogged acidic soil would soon fill with acidic water. If the pit was dug in the peat draining area at the edge of the bog, it would soon fill with peat draining water. Whatever the source of the acidic water, the acid in the water would prevent acorns from leaching, would make horrible tasting beer, would make salt extraction through evaporation impossible...

So why were so many fulachta fiadh built in waterlogged acidic soils and on the edges of bogs? . . .

Bogs are rain fed (ombrotrophic). They need poorly-drained areas, a climate where precipitation exceeds evaporation, and a nutrient-poor environment that favors peat mosses in their ecologic competition against higher plants. Growth of higher plants is also curbed by peat mosses themselves because they bind available nutrients and render the bog water acidic. The acidity comes from the so called low-molecular-weight organic acids (LMWOAs): Formic, acetic, pyruvic, oxalic, malonic, and succinic acids. The amount of these acids in bog water is so high that the pH of bog water is 3-4. This is really acidic indeed. If this bog water is then exposed to the sunshine, it will get even more acidic. . . . solar radiation will degrade organic matter found in bog water and form more low-molecular-weight organic acids (LMWOAs), making the bog water even more acidic. How much more acidic? Not sure what the final pH of the bog water exposed to the sunshine is. But it is definitely low enough to serve as a very good pickling solution.

Pickling is the process of preserving or expanding the lifespan of food by immersing in pickling brine (salty and acidic liquid). If the food contains sufficient moisture, a pickling brine may be produced simply by adding dry salt which draws water out of the food creating salty liquid. Natural fermentation at room temperature, by lactic acid bacteria, produces the required acidity creating salty and acidic liquid - pickling brine. If the food does not contain sufficient moisture, pickling can also be achieved by immersion of food in some salty acidic liquid, such as mixture of salty water and vinegar. If you want your pickling to be successful, the pH of the pickling brine has to be 4.6 or lower, which is sufficient to kill most bacteria. The pickling procedure will typically affect both food's texture and flavor but it will preserve otherwise easily perishable food for months or longer. Foods that can be pickled include meats, fruits, eggs, vegetables and milk products like cheese. . . . 

Yes but what does pickling has to do with bog water? Who would use bog water for pickling? Well as it turns out a lot of people. And some of them could have been the Bronze Age Irish builders of fulachta fiadh. 

As I already said in my post "Fulacht fiadh - meat and fish curing facility", the ancient Irish probably used both salt and smoke curing of meat and fish as a means of preserving it long term. But there is another way Ancient Irish could have preserved food long term without need for salting or smoking.

They could have buried it into the peat bog.

It turns out that there are multiple historical examples of food storage in bogs as a preservative and that it can also be used in the tanning of leather.

ATLAS Measures The Top Quark Mass With Hadrons

The most precise ways to measure the top quark mass are with leptonic decays. But, while hadronic decay measurements are harder to do and less precise, they make the overall measurement more robust, because the systemic errors involved in hadronic decay measurements are largely independent of the systemic errors involved in leptonic decay measurements. 

The top-quark mass is measured in the all-hadronic top-antitop quark decay channel using proton-proton collisions at a centre-of-mass energy of s√ = 8 TeV with the ATLAS detector at the CERN Large Hadron Collider. The data set used in the analysis corresponds to an integrated luminosity of 20.2 fb−1. The large multi-jet background is modelled using a data-driven method. The top-quark mass is obtained from template fits to the ratio of the three-jet to the dijet mass. The three-jet mass is obtained from the three jets assigned to the top quark decay. From these three jets the dijet mass is obtained using the two jets assigned to the W boson decay. The top-quark mass is measured to be 173.72 ± 0.55 (stat.) ± 1.01 (syst.) GeV.

ATLAS Collaboration "Top-quark mass measurement in the all-hadronic tt¯ decay channel at s√ = 8 TeV with the ATLAS detector" (February 24, 2017).

The combined error of the ATLAS hadronic top quark mass measurement is about ± 1.15 GeV. This is higher than the leptonic measurements, but not outrageously so and is 37% of the error for the CMS hadronic measurement, for which the measured value was quite similar. Honestly, the latest CMS leptonic top quark mass error estimate is suspiciously low.

My latest summary of top quark mass measurements can be found in a December 16, 2016 post. The highlights of that post were as follows:

The combined ATLAS result from the √ s = 7 TeV dileptonic and semileptonic tt¯ measurements yields a value of mtop = 172.99 ± 0.48 (stat) ± 0.78 (syst) GeV. 

Additional precision is to be expected with the inclusion of √ s = 8 TeV measurements. The combined CMS result of mtop = 172.44 ± 0.13 (stat) ±0 .47 (syst) GeV is based on all √ s =7 and 8 TeV measurements performed in the three standard tt¯ decay channels. The results of both experiments are in good agreement. . . .

A previous low precision CMS report using a hadronic channel not included in the CMS average above is here. It reported a top quark mass of 173.5 ± 3.13 GeV. 

The final Tevatron mass measurement for the top quark was 174.30 ± 0.65 GeV.

The combined ATLAS error is ± 0.92 GeV. The combined CMS error is ± 0.49 GeV. The range of the independent average top quark mass measurements is 1.86 GeV. . . .

The inverse error weighted average of the three main results plus the CMS hadronic channel is 173.20 GeV.

Excluding the CMS hadronic channel (which there is no good reason to do in an error weighted measurement), the inverse error weighted average is 173.18 GeV. . . .

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

The expected value of the top mass from the formula that the sum of the square of each of the fundamental particle masses equals the square of the Higgs vaccum expectation value (a less stringent condition because the fermion and boson masses don't have to balance), given the global average Higgs boson mass measurement (and using a global fit value of 80.376 GeV for the W boson rather than the PDG value) is 173.73 GeV. The top quark mass can be a little lighter in this scenario because the global average measured value of the Higgs boson mass is a bit heavier than under the more stringent condition.

The latest hadronic measurement of the top quark mass from ATLAS is in the high end, and is very close to the much less precise CMS hadronic measurement, and to the theoretically predicted value that I generated. Because of the significant margin of error, the new ATLAS hadronic measurement is consistent with all of the other recent measurements of the top quark mass. 

Smallpox And Salmonella Did More To Wipe Out Native Americans Than Genocide

Something like 95% of Native Americans died when Europeans arrived in the New World.

But, in North America, at least, the leading cause of death was an epidemic of smallpox from 1775 to 1782 that raced ahead of European colonists from the Atlantic Coast to the Pacific Coast. 

This epidemic was not intended by the colonists as a means of destroying the existing population, nor was it even really well understood. While the germ theory of disease had been proposed at that point, it was not widely accepted.

This isn't to say that Europeans did right by Native Americans before or after this epidemic. But, the bulk of the Native American deaths caused by the Europeans in North America were due to the inadvertent spread of diseases to which Native American populations never exposed to them were far more vulnerable than Europeans who had 8,000 years or so of natural selection at work building their immune systems' ability to defend against these diseases. And, the military superiority of Europeans in the century or so of conquest called "the Indian Wars" that followed, had as much to do with the residual impacts of this devastating loss of life due to new infectious diseases as it did to do with weapons or tactics.

According to the linked Wikipedia article:

The 2010 census found 2,932,248 Americans who identified themselves as being Native American (or Alaskan Native), about 0.9% of the U.S. population. No consensus exists on how many native people lived in the Americas before the arrival of Columbus, but extensive research has been and continues to be conducted. Estimates on the population of pre-Colombus North America range from a low of 2.1 million (Ubelaker 1976) to 7 million people (Russell Thornton) to 18 million (Dobyns 1983).

As the direct result of infectious diseases, conflict with Europeans, wars between tribes, assimilation, migration to Canada and Mexico, declining birth rates, the numbers of Native Americans dropped to below half a million in the 19th century. Scholars believe that the overwhelming main causes were new infectious diseases carried by European explorers and traders. Native Americans had no acquired immunity to such diseases, which had been chronic in Eurasian populations for over five centuries. For instance, some estimates indicate case fatality rates of 80–98% in Native American populations during smallpox epidemics.

The United States Census Bureau (1894) provided their estimate of deaths due specifically to war during the 102 years between 1789 and 1891, including 8,500 natives and 5,000 whites killed in "individual affairs": 

The Indian wars under the government of the United States have been more than 40 in number. They have cost the lives of about 19,000 white men, women and children, including those killed in individual combats, and the lives of about 30,000 Indians. The actual number of killed and wounded Indians must be very much higher than the number given... Fifty percent additional would be a safe estimate.

One important matter attributable to neither combat death nor disease that none of the sources above address is the loss of life, loss of land, loss of culture, and general privation associated with the relocation of Native Americans to reservations far less desirable to them than their ancestral lands, mostly during the 19th century. Such as the relocation of the Cherokee Nation by Andrew Jackson in 1838 and 1839 known as the Trail of Tears.

In a similar vein, another European disease spread long before the germ theory of disease was understood probably causes massive deaths among the people of what is now Mexico. According to Scientific American magazine, hard evidence now linked the collapse of Aztec society following first contact with Spanish conquistadors with an outbreak of Salmonella, to which that society was not adapted either in food preparation methods or in their immune systems.

One of the worst epidemics in human history, a sixteenth-century pestilence that devastated Mexico’s native population, may have been caused by a deadly form of salmonella from Europe, a pair of studies suggest. 

In one study, researchers say they have recovered DNA of the stomach bacterium from burials in Mexico linked to a 1540s epidemic that killed up to 80% of the country's native inhabitants. The team reports its findings in a preprint posted on the bioRxiv server on February 8. . . .

In 1519, when forces led by Spanish conquistador Hernando Cortés arrived in Mexico, the native population was estimated at about 25 million. A century later, after a Spanish victory and a series of epidemics, numbers had plunged to around 1 million. The largest of these disease outbreaks were known as cocoliztli (from the word for ‘pestilence’ in Nahuatl, the Aztec language). Two major cocoliztli, beginning in 1545 and 1576, killed an estimated 7 million to 18 million people living in Mexico’s highland regions. 

“In the cities and large towns, big ditches were dug, and from morning to sunset the priests did nothing else but carry the dead bodies and throw them into the ditches,” noted a Franciscan historian who witnessed the 1576 outbreak. 

There has been little consensus on the cause of cocoliztli—although measles, smallpox and typhus have all been mooted. In 2002, researchers at the National Autonomous University of Mexico (UNAM) in Mexico City proposed that a viral haemorrhagic fever, exacerbated by a catastrophic drought, was behind the carnage. They compared the magnitude of the 1545 outbreak to that of the Black Death in fourteenth-century Europe.

In an attempt to settle the question, a team led by evolutionary geneticist Johannes Krause at the Max Planck Institute for the Science of Human History in Jena, Germany, extracted and sequenced DNA from the teeth of 29 people buried in the Oaxacan highlands of southern Mexico. All but five were linked to a cocoliztli that researchers think ran from 1545 to 1550. 

Ancient bacterial DNA recovered from several of the people matched that of Salmonella, . . . Further sequencing of short, damaged DNA fragments from the remains allowed the team to reconstruct two genomes of a Salmonella enterica strain known as Paratyphi C. Today, this bacterium causes enteric fever, a typhus-like illness, that occurs mostly in developing countries. If left untreated, it kills 10–15% of infected people. . . . 

Krause and his colleagues’ proposal is helped by another study posted on bioRxiv . . . which raises the possibility that Salmonella Paratyphi C arrived in Mexico from Europe. A team . . . collected and sequenced the genome of the bacterial strain from the remains of a young woman buried around 1200 in a cemetery in Trondheim, Norway. It is the earliest evidence for the now-rare Salmonella strain, and proof that it was circulating in Europe . . . 

The existence of Salmonella Paratyphi C in Norway 300 years before it appeared in Mexico doesn’t prove that Europeans spread enteric fever to native Mexicans, says Schroeder, but that hypothesis is reasonable. A small percentage of people infected with Salmonella Paratyphi C carry the bacterium without falling ill, so apparently healthy Spaniards could have infected Mexicans who lacked natural resistance. Paratyphi C is transmitted through faecal material, and a collapse of social order during the Spanish conquest might have led to the poor sanitary conditions that are ripe for Salmonella spread, Krause and his team note in the paper. 

Even in modern times, mass deaths on this scale usually accompanies first contact experiences of "uncontacted peoples" such as certain remaining Amazonian tribes. 

Harappan Y-DNA Leak

Ancient Harappan DNA is being analyzed right now for publication later this year. Leaks from the lab about the Y-DNA type of these samples (for what reliability one is inclined to give them) are as follows:

Over at Anthrogenica, there's now two members who say they've heard from people associated with the Rakhigarhi investigation that the Rakhigarhi aDNA samples were overwhelmingly L-M20. . . .

"So I don't know if this has been discussed, but I heard from somebody who knows an archeologist at the Rakhigarhi site. 

They are going to release a paper later in the year and 80-90% of the samples were y-HG L-M20. 

I will inquire for more details. I can't verify the authenticity of the man's claims.". . .

Khanabadoshi's choice of expression has got me confused. Eurogenes had mentioned 12 ancient samples were genotyped from the Rakhigarhi site. Neither 80% nor 90% thereof produce very round figures, at 9.6 to 10.8 ancient persons. Does it imply the remaining 10-20% samples were female, so that all ancient males were L-M20. Or does it mean that oddly all of the samples are exclusively male, with the remaining 1-2 ancient people being some other Y haplogroup? (Since Chad Rohlfsen has said L and R2 above, though it's not clear if the R2 is meant predictively or based on a rumour or leak. Razib Khan had predicted H and L a couple of years back.)

Y-DNA haplogroup L-M20 is reasonably common Y-DNA haplogroup in parts of Pakistan and India where the Harappan civilization once thrived, this is is not a stunning result, although peak frequencies in that region today are only about 25%, and are between 10% and 20% for most of the former Indus River Valley civilization area.  (Of course, there is a very good chance that this is not an "independent random" sample and may include distantly related individuals, which would naturally tend to skew towards one haplogroup being dominant.)

Y-DNA haplogroup L is a sister clade to Y-DNA haplogroup T.

Y-DNA haplogroup R1a is fairly common in the region today and widely attributed to Indo-Aryan invaders, so it shouldn't be found in these samples. 

Y-DNA haplogroup R2 is fairly common in Southern and Eastern India as indicated below, and with some notable exceptions is not that strongly tied to the Indus River Valley. 

Y-DNA haplogroup H is a leading Y-DNA type in India, widely believed to be autochronous, and showing up in Pakistan as well although with how much antiquity it is hard to know. An absence of Y-DNA haplogroup H would tend to show relative low levels of contact with the southern India, where the Dravidian languages are now spoken.

UPDATE February 27, 2017:

One of the big questions presented if Y-DNA R2 is absent from the Harappan sample is when R2 made its way into the Indus River Valley gene pool. We think we know from ancient DNA that Y-DNA R, in general has origins somewhere around the Altai.

Y-DNA R2 via the Wikipedia link above.

We also have no evidence of Y-DNA R2 on the steppe where numerous ancient Y-DNA samples from Mesolithic times to the present show Y-DNA R1a and R1b, which makes the arrival of Y-DNA R2 with the Indo-Aryans or for that matter even Indo-Iranians, more generally, seem improbable. Indeed, it seems to be common in places where Indo-Aryan genetic influence is lowest.

Yet, the South Asian gene pools seems relatively stable over the last 2500 years or so. And, none of the historic era migrations can account for its presence in any of the historically attested populations that migrated to South Asia.

Y-DNA R2 is a pretty much private South Asian haplogroup. Based upon its distribution and the admittedly unreliable measure of mutation rate dating, it R2 might have emerged in South Asia itself ca. 28,200 years ago, and thus arriving prior to the LGM during the Upper Paleolithic era. The dominant sub-group R2a dates to about 12,000 years ago and the most instances of the basal paragroup R2* by far (6) are in Pakistan, a number that is probably an underestimate due to sampling biases against South Asia and in favor of Europe and Russia.

Notable Views Regarding Physics

Preface

If you review a large amount of information about a subject and don't have an opinion, you aren't paying attention. Needless to say, I have opinions about a great many matters that I have reviewed at the "tree level" over the years in the area of physics.

If you are a long time reader of this blog, you know the views that I have expressed on a variety of notable issues in physics. But, if you are relatively new to this blog, you might be less familiar with these views. 

It is not my purpose to mislead anyone into thinking that there is a scientific consensus regarding an observation that I make that may be a minority view regarding a controversy or issue, or may even be one that I am the only person currently actively advocating. And, anyone reading this blog should know the assumptions, preconceptions and hypotheses that I come to my coverage holding.

Also, I want to make clear that none of my views on these physics issues are set in stone. They represent my current synthesis of the available evidence. I have changed my mind about some of them in the past, and no doubt will in the future as new evidence becomes available. Each new data point refines the picture, sometimes confirming it with greater certainty, sometimes providing greater detail, and sometimes resulting in a paradigm shift.

This post is a summary of conclusions. It does not purport to even attempt to cite to posts at this blog where I marshal evidence in favor of a view or analyze why I believe it to be correct. This has happened over the course of many hundreds of posts and would be too time consuming and voluminous to include here.

Substance - My Most Notable Views About Physics

I. Gravity, Dark Matter, Dark Energy and Astronomy

A. In my view the most unimportant unsolved problem in fundamental physics is how the phenomena attributed to dark matter arise.

B. There are two primary paradigms: particle based dark matter theories and gravity modification theories. The available evidence does not refute all models advanced in either approach, although much of the potential dark matter parameter space has been ruled out by observation and analysis, and some gravity modification theories have likewise been ruled out.

C. I believe that a gravity modification theory is considerably more likely than a particle based theory to explain dark matter phenomena.

D. I believe, at a lower level of certainty, following the work of Deur, that:

(1) the correct gravity modification arises from a quantum gravity theory that conceptualizes gravity as an exchange of gravitons rather than primarily as a geometric bending of space-time;

(2) this quantum gravity theory differs from the predictions of general relativity predominantly in weak gravitational fields (as opposed, for example, to near the Big Bang or black holes);

(3) the quantum gravity modification largely arises from the failure of general relativity to accurately reflect second and greater order effects arising from graviton interaction with other gravitons in a manner analogous to gluon interactions with other gluons;

(4) in principle this quantum gravity theory introduces no new fundamental constants not found in GR (although it may operationally need one or two constants that are in practice derived even though they could in principle be determined from existing constants);

(5) in this theory the amount of ordinary matter and the shape of the geometric distribution of matter both impact the second order quantum gravity effects;

(6) much or all of the effects of dark energy result from gravitons being diverted to make gravitational pulls stronger in ways that manifest in dark matter phenomena, leading to gravitational forces between systems that manifest dark matter phenomena to be weaker than they would be without this effect; and

(7) there are solid indications that the amount of dark energy or the size of the cosmological constant, as the case may be, is materially overestimated experimentally, which makes it more likely that substantially all dark energy effects are side effects of dark matter phenomena.

E. If, the less probable case is true and in fact, gravity is not modified and the source of dark matter is a particle:

(1) dark matter phenomena are predominantly the product of not more than two kinds of particles (a fermion singlet (which may or may not be composite) and a boson that interacts only with dark matter), and quite possibly only one kind of particle (indeed, most likely only one kind of particle); 

(2) those particles are warm dark matter scale for the fermion or less; and

(3) the dark matter particles have essentially no non-gravitational interactions with ordinary matter through any of the three Standard Model forces (electromagnetic, strong and weak).

II. Cosmology

A. In my view, the most likely explanation for the matter-antimatter asymmetry in the universe is that there is an antimatter dominated universe "before" the Big Bang in which the second law of thermodynamics runs in the other direction that balances the matter dominated nature of our own universe. This implies that a new source of extreme CP violation is unnecessary. But, I do not hold this view with a high level of confidence.

B. In my view, the evidence to support the events of the early moments of the Big Bang prior to Big Bang nucleosynthesis, including "inflation" is not solid enough to constitute scientific proof and is merely a plausible hypothesis.

C. I believe that the multiverse and anthropic principle are being used in fundamentally unscientific ways at this time.

III. Neutrino Physics

A. I think that neutrinos are very unlikely to have Majorana mass.

B. I think that neutrinos have a "normal" mass hierarchy.

C. I think that cosmology based caps on the sum of the neutrino masses are accurate and can be integrated with other data to accurately estimate the neutrino masses.

D. I think that we don't understand the mechanism of neutrino mass generation or neutrino oscillation beyond the current phenomenological model. But, I think that seesaw models of neutrino mass are almost surely wrong. I think that there is a reasonable possibility that some sort of boson mediates neutrino oscillation.

E. I think that neutrino oscillation almost surely has a CP symmetry violating term.

F. I think that neutrino oscillation does not involve any maximal mixing angles.

G. I think that neutrinoless double beta decay never happens, nor do any other forms of sub-GUT scale lepton number violation or baryon number violation (such a proton decay).

H. I think that there is probably not a right handed neutrino.

IV. Quantum Mechanics And Space-Time

A. Entanglement inherently requires a surrender of at least one of three things: causality, locality and reality. I am not nearly so convinced that causality and locality need to be maintained as many physicists.

B. I think that the non-speed of light paths in the particle propagator of quantum mechanics suggests that the picture of space-time are perfectly smooth and local is likely to be incorrect.

C. I think that the four dimensional nature of space-time may be emergent, but that there are unlikely to be more than four or five dimensions of space-time, and that there are no compactified dimensions.

D. I am not perfectly convinced that quantum mechanical randomness is not just extremely chaotic (in a mathematical sense of a deterministic system highly sensitive to slight changes in initial conditions) rather than truly random behavior.

V. Beyond The Standard Model Theories

A. I believe that some of the most notable experimental anomalies which physics are dealing with today, such as the muon g-2 problem and the muonic proton radius puzzle, are due to some combination of experimental error and a failure to properly apply existing fundamental physical laws to the problems properly, rather than to beyond the Standard Model Physics.

B. I believe that so called "problems" such as the "hierarchy problem" and the "strong CP problem" are not problems at all that need to be solved and are unsound at a basically philosophical level in their very formulation.

C. I believe that there are deeper theories that can explain the relationship of the Standard Model constants, particles and forces to each other from a more fundamental set of rules and constants. For example:

(1) I think that the sum of the square of the fundamental particle masses is functionally related to the Higgs vacuum expectation value.

(2) I think that at least the charged fermion masses relative to each other dynamically through a process that primarily involves W boson interactions and reproduces a relationships approximately captures in Koide's rule.

(3) I think that it is likely that the CKM matrix can accurately be parameterized with one real parameter and one complex parameter.

(4) I think it is plausible that the CKM matrix parameters are related functionally, in some way, to the PMNS matrix parameters.

(5) I think it is plausible that it may be possible to determine the CP violating phases of the CKM matrix and PMNS matrix from first principles.

D. I believe that the barriers to quantum gravity involve more of a shortage of computational tools and lack of creativity, than they do any fundamental theoretical problem.

E. I think that beyond the Standard Model fundamental particles that do not serve merely as preons for Standard Model fundamental particles are generally ill motivated. We might be missing one or two, but if my conjectures regarding dark matter are correct, we don't need any more fundamental particles, and certainly not the multitude suggested by SUSY theories.

F. I think that supersymmetry and supergravity do not accurately describe reality and merely constitute toy models useful for thinking about particle physics to use in more realistic models.

G. I think that there are some operative principles for applying quantum chromodynamics that we do not yet know which are necessary to understand the non-observation of glueballs and the spectrum of scalar and axial vector mesons.

H. I think that string theory is incorrect but may provide valid insights.

Big Cities Are Something New Under The Sun

There is nothing new under the sun.

- Ecclesiastes 1:9.

But, one quite new phenomena (certainly since the Hebrew Bible Book of Ecclesiastes was written ca. 450 BCE–180 BCE, probably incorporating older oral traditions) has been the rise of the big cities. 

For example, Denver, Colorado, where I live, which isn't particularly exceptional as large cities go, is more than twice as large as the largest city in the world as of 1800 CE and is three times as large as London was in 1800. London reached the current population of Denver in the 1850s, during the Victorian era (at which time it was the largest city in the world). New York City reached the current population of Denver in 1890 at which time it was the largest city in the United States; Denver has about three times the population that New York City did in 1850.

* The largest city in the world in 2000 BCE was Memphis, Egypt with 60,000 people.

* By 1000 BCE, Memphis had grown to 100,000 people, tied with Babylon in modern day Iraq, and the largest city in the world was Thebes, Egypt with 120,000 people.

* In 100 CE, the largest city in the world was Rome, Italy with 1,000,000 people followed by Alexandria, Egypt with 500,000, and Luoyang, China with 420,000.

* In 1500 CE, the largest city in the world was Beijing, China with 672,000 people, followed by Vijayanagar, India with 500,000, followed by Cairo, Egypt with 400,000. Paris, France which was the largest city in Europe in 1500 CE had a population of about 185,000 people.

* As of 1800 CE, the largest city in the world was Beijing, China with 1,100,000 people, followed by London with 861,000, Guangzhou, China with 800,000 an Tokyo (Edo), Japan with 685,000.

* In 1975 CE, Tokyo was the largest city with 23,000,000 people and New York City followed with 17,100,000 people.

All of these data points represent urbanized areas and not just city-proper populations. The link is to the supplemental materials from:

Meredith Reba, et al., "Spatializing 6,000 years of global urbanization from 3700 BC to AD 2000", 3 Scientific Data 160034 (June 7, 2016).

Wikipedia also has a list of historical city sizes going back as far as there is reliable information that restates the two prior studies relied about by Reba and also a couple of additional sources, and for Europe, here.

The article does seem to omit a few large pre-Columbian New World cities like Mexico City, formerly known as Tenochtitlan in the Aztec period, which had a population of 200,000 to 350,000 in 1500 CE (which would have been the fourth largest city in the world) and Cahokia which had a population 40,000 in ca. 1000 CE (the largest city in the territory that would become the United States until Philadelphia ca. 1780 CE).

Ancestry Analysis In Han Chinese Populations With Functional Immunity Genes

The following excepts are from the results section of a new open access paper in variation in functional immune system genes call KIR to show ancestral relationships of populations, which will be cited at the end of this post.

Global Population Genetics And The Mysterious Distribution Of KIR Genetic Clusters

Its finding first confirmed a divide between West Eurasians, South Asians, Papuans, Oceanians and Native Americans on one hand, and East Asians, Southeast Asians and Africans on the other.

In the phylogenetic tree, we could clearly find two main clusters. The smaller cluster consisted of Palestinian, Adygei, Tuscan, Hazara, Sardinian, North Italian, Barusho, Karitiana, Pima, Pathan, Papuan and Melanesian. Eastern Chinese Han gathered with Jilin Han in another cluster, following the sub branch containing Shanghai Han, Miao, Japanese, Hezhen, Naxi, Daur and Tujia, then with Yunnan Han and Shaanxi Han. Interestingly, all 7 African populations were genetically closer to populations from East Asia than West Europe, America and Pacific Ocean[.] 

The somewhat atypical alignment of continental groups in their KIR genes may reflect selective sweeps that impacted some continental regions, but not others. The East Asian, Southeast Asian and African one would presumably be the ancestral one, while the other would have the more derived version of KIR genes. But, the source of the selective pressure would have to be quite ancient to include Papuans.

Han Population Genetics And History

The paper then looked at relationships of Han Chinese populations within China. This corroborates a mass migration of the Eastern Chinese to Northeast China, and the affects of admixture with British nationals in Hong Kong.

In particular, the Jilin Han who are ethnically Han Chinese people who live in Jilin province immediately to the north of North Korea migrated there as part of a deliberate plan to demographically overwhelm the ethnically Korean and ethnically Manchurian and linguistically Tungistic people who are indigenous to the region. These peoples have population genetic continuity in the region going back to the Mesolithic era, and managed to remain ethnically distinct within the sphere of greater Chinese influence. This area is also the likely penultimate source (before Korea) of the Yayoi contribution to the Japanese people whose ethnic and linguistic identity is not entirely clear. We also have evidence of a catastrophic disease outbreak of some kind in this region around 3000 BCE, just as the Holocene climate optimum was ending.

There was a similar migration of west to east into the Sichuan area by ethnically Han Chinese people at roughly the same time.

Han Chinese expansion pretty much culturally obliterated any trace of pre-existing ethnic populations in much of Eastern China and indeed substantially replaced them on a demic basis as well in a large part of China, although there are numerous intra-Han Chinese distinctions based upon regional topolects which share a common set of Chinese characters as the central part of their written language (although even these characters are not entirely uniform across the Chinese linguistic area).

Some of this, as the paper notes, is relatively recent (ca. 1650 CE to 1900 CE and later), while some of this is much more ancient.

A lot of this expansion took place between 4800 BCE and 3000 BCE during which half a dozen Y-DNA haplogroups that account for 65% of the Chinese population experienced a rapid expansion, that also coincides with the domestication of soybeans in Northern China, the expansion of millet agriculture, and the mastery of beer brewing. Climate factors around this time also provided a push factor that encouraged southern migration as "barbarian" populations migrated south placing pressure on the existing populations of Northern China to do likewise. This period of extremely rapid genetic expansion ends corresponds roughly to the Yangshao culture, which was replaced by the Longshan culture ca. 3000 BCE at the end of the Holocene climate optimum. Population growth apparently continued for another 1000 years during the Longshan period, and in both the Yangshao and Longshan cultures, millet, pig and dogs were the primary sources of sustenance, they cultivated silkworms, and they made minor use of rice, but had few cattle, sheep or goats. Soybeans were also probably an important source of sustenance in these cultures, but this is harder to establish archaeologically because soybean waste does not leave as much of an archaeological trace.

Rice farming was expanding around the same time, in parallel, in Southern China, which also cultivated pigs, peaches and chickens (which appear to have been domesticated in Taiwan).

Legendary history starts to receive some archaeological corroboration in the Yellow River region by about 1900 BCE, around the time that the Chinese Bronze age commenced with the Erlitou culture (which arguably corresponds to the legendary Xia culture, which is conventionally dated to about 150 years later). Ancient DNA evidence suggests that the population genetic makeup of the Han Chinese in China's central plains in northern China was pretty much in place in its modern form by at least 1000 BCE.

The only trace of what came before seems to be the residual cultural divide between populations influenced by the more individualist oriented millet and wheat farming cultural influence in the North which contrasts with the more collective cultural values associated with rice farming in the South, with some residual population genetic distinctions in the South.

Using KIR as the panel of genetic marker, the results showed that Eastern Han from Jiangsu province had the closest relationship with Jilin Han, followed by Shanghai Han, indicating that Eastern Han shared a common ancestry, which was consistent to the findings based on other genetic markers, such as autosomal STRs and Y-STRs by Yao et al. 

The notable association of Eastern Han with Jilin Han was confirmed by the famous large-scale migration literally called “Crashing into Guandong”. Since A.D. 1,650, to control the rapid expansion of Chinese Han population, Han from Eastern China was promoted by the national policy to migrate to Northeastern China. As a result, Chinese Han accounted for 80% of the total northeastern Chinese during the 18th century. Besides, that Eastern Han was genetically close to Shanghai Han could be explained by the close geographic location and long-term cultural interaction. 

We also found Hong Kong Han displayed the farthest genetic distance to Eastern Han compared to other Han populations, obviously, which could be explained by the fact that Hong Kong Han mixed with lineage from the United Kingdom. The genetic characteristics of Eastern Han revealed that subpopulations sharing the same ancestry may have genetically closer relationships than geographically close groups. 

Wen et al. revealed the southward expansion of Han on the basis of variance of Y-chromosomal and mitochondrial DNA. Chen et al. analyzed genome-wide SNP variation and demonstrated the population stratification of Hans from 10 provinces including over 6,000 Han Chinese samples. Both studies indicated the north-south migration of Han Chinese. In this research, the relationships between Eastern Han populations and others worldwide were emphasized. The strongest association between Eastern Han and Jilin Han showed the impact of historical event “Crashing into Guandong”, which was a south to north migration route in the history, on genome polymorphisms. 

Our research utilized KIR as markers to provide new evidences for illustrating the potential Han dispersal. 

The paper is Caiyojong Yin, et al., "Genetic polymorphism and evolutionary differentiation of Eastern Chinese Han: a comprehensive and comparative analysis on KIRs" 7 Scientific Reports 42486 (February 16, 2017).

Verlinde's Emergent Gravity Doesn't Work

Verlinde sought to reproduce the successes of other modified gravity theories in a variant of his entropy based gravity theories called "emergent gravity" which arises from quantum entanglement.

The entanglement based "emergent gravity" theory itself is discussed in two recent posts:

* Emergent Gravity (November 30, 2016)
* Quick Physics Hits (November 14, 2016)

Verlinde's entropic gravity theories that were predecessors to emergent gravity were discussed in two 2012 posts:

* A Review of Fundamental Physics in 2012 (December 24, 2012)
* Two Provocative Papers On Gravity (December 4, 2012)

Unfortunately, "emergent gravity" doesn't reproduce the observed data.

Verlinde (2016) has recently proposed that spacetime and gravity may emerge from an underlying microscopic theory. In a de Sitter spacetime, such emergent gravity (EG) contains an additional gravitational force due to dark energy, which may explain the mass discrepancies observed in galactic systems without the need of dark matter. For a point mass, EG is equivalent to Modified Newtonian Dynamics (MOND). We show that this equivalence does not hold for finite-size galaxies: there are significant differences between EG and MOND in the inner regions of galaxies. We confront theoretical predictions with the empirical Radial Acceleration Relation (RAR). We find that (i) EG is consistent with the observed RAR only if we substantially decrease the fiducial stellar mass-to-light ratios; the resulting values are in tension with other astronomical estimates; (ii) EG predicts that the residuals around the RAR should correlate with radius; such residual correlation is not observed.

Federico Lelli, Stacy S. McGaugh, and James M. Schombert "Testing Verlinde's Emergent Gravity with the Radial Acceleration Relation"(February 14, 2017).

Another study looking at a different set of data with different investigators reaches basically the same conclusion.

It was recently proposed that the effects usually attributed to particle dark matter on galaxy scales are due to the displacement of dark energy by baryonic matter, a paradigm known as emergent gravity. This formalism leads to predictions similar to Modified Newtonian Dynamics (MOND) in spherical symmetry, but not quite identical. In particular, it leads to a well defined transition between the Newtonian and the modified gravitational regimes, a transition depending on both the Newtonian acceleration and its first derivative with respect to radius. Under the hypothesis of the applicability of this transition to aspherical systems, we investigate whether it can reproduce observed galaxy rotation curves. We conclude that the formula leads to marginally acceptable fits with strikingly low best-fit distances, low stellar mass-to-light ratios, and a low Hubble constant. In particular, some unobserved wiggles are produced in rotation curves because of the dependence of the transition on the derivative of the Newtonian acceleration, leading, even in the most favorable case, to systematically less good fits than MOND. Then, applying the predicted transition from emergent gravity in a regime where it should be fully applicable, i.e. in spherical symmetry and outside of the bulk of matter, we show that the predictions for the secular advances of Solar System planets' perihelia are discrepant with the data by seven orders of magnitude, ruling out the present emergent gravity formalism with high confidence.

Aurelien Hees, Benoit Famaey, and Gianfraco Bertone, Emergent gravity in galaxies and in the Solar System (February 14, 2017)

Losing Neanderthal mtDNA Through Drift (An Old Result)

The Facts Of Our Neanderthal Genetic Inheritance

Not a single modern human today has Neanderthal mtDNA and not a single sample of ancient mtDNA from a modern human is derived from a Neanderthal either. Likewise, not a single man on Earth today, or a single modern human's ancient DNA harbors Neanderthal Y-DNA. Yet, about 4% of the autosomal DNA on non-Africans is derived from Neanderthals and some ancient DNA samples have elevated levels of autosomal Neanderthal DNA.

A Random Genetic Drift Explanation For The Lack Of Neanderthal mtDNA

How could this happen?

A Letter to the Editor of the journal American Human Genetics from Magnus Nordborg entitled On the Probability of Neanderthal Ancestry, written in 1998 before we knew that humans had autosomal Neanderthal DNA discusses this point (starting at page 22 in the linked pdf):

Two simple scenarios for human demography were used—namely, constant population size and constant ancient-population size followed by exponential growth 50,000 years ago. For both cases, the effective number of females in the constant population was assumed to be 3,400, growing exponentially to for the latter 8 5 # 10 case. These parameters were chosen so that the probability would be high that Te lies within the range 100,000–200,000 years, when a generation time of 20 years is assumed. The age of the sampled Neanderthal, ts, was assumed to be 30,000–100,000 years (the recovery of DNA more ancient than 100,000 years seems highly doubtful [Krings et al. 1997]). I argue below that the absolute values of all these parameters are of considerably lesser importance than their relative values. Table 1 gives the results for models of random mating. As expected, the probability that both a compatible topology and an extreme difference between Te and Tr would be observed is low, and, therefore, the hypothesis that modern humans and Neanderthals were a randomly mating population may be rejected. However, closer inspection reveals the more interesting fact that the topology alone may not be unlikely. The reason for this is that, unless the sampled Neanderthal lived long after human populations had started to grow exponentially, most of the modern mtDNA lineages would have coalesced at ts: if, for example, the modern sample only had two ancestors who were contemporary with the sampled Neanderthal, it would not be surprising if they were monophyletic (probability of 1/3). A large difference between Te and Tr, on the other hand, is always unlikely under random mating. . . .  

For the constant–population-size model, for example, assume that Neanderthals and anatomically modern humans merged 1 coalescent-time unit ago (equivalent to tm = 68,000 years, for the population size used above) and that Neanderthals composed 25% of the new population. Then, the probability that all Neanderthal mtDNA was lost through drift is .52 (the probability that Neanderthal mtDNA was not in the sample [calculated as above] is the same, to two decimal places). At the same time, each nuclear locus, for which the coalescence-time scale is four times slower, would have lost all Neanderthal alleles with probability .10 and would have become fixed for them with probability 9.8*10^-5. Thus, 90% would still be segregating for Neanderthal alleles. In conclusion, data such as those shown in figure 1 shed little light on the issue of replacement versus interbreeding, unless the number of ancestors of the sample was large throughout the periods of interest. This is part of a general problem: in order to estimate gene flow, a large sample is needed, and, in order to estimate ancient-gene flow, a large ancient sample is needed. According to coalescent theory, large ancient samples usually cannot be obtained by the sampling of modern populations. The rate of coalescence is quadratic in the number of ancestors and linear in the inverse of the population size. Thus, the expected number of ancestors of a sample usually decreases rapidly as earlier time periods are studied. Exceptions include exponentially growing populations, in which the number of ancestors may be large shortly after the onset of growth (reviewed in Donnelly and Tavare´ 1995; Marjoram and Donnelly 1997). In the present case, it seems clear that the statistical power to detect interbreeding that took place before the human population started to grow exponentially is close to zero.

In fact, I am skeptical that modern humans were not experiencing exponential population growth around the time of Neanderthal admixture and personally believe that a more restrictive admixture model is what kept Neanderthal mtDNA out of the modern human gene pool.

A Social Explanation For The Lack Of Neanderthal mtDNA

Specifically, I think that almost all Neanderthal-modern human admixture involve short term sexual encounters (which may or may not have been consensual) in which the female in the couple remained a part of a tribe belonging primarily to her own species, rather than in long term marital relationship or merged tribes.

Thus, Neanderthal hybrids born into modern human tribes almost all had modern human single mothers, and Neanderthal hybrids born in Neanderthal tribes almost all had Neanderthal single mothers.

Of course, neither model needs to be 100% true. 

The percentage of autosomal Neanderthal DNA in modern humans suggests that the Neanderthal fraction of the autosomal DNA of the initial modern population was probably 12% or less, rather than the 25% used to determine that there was a chance of Neanderthal mtDNA due to drift during period of more or less constant population.

Suppose also that two-thirds of Neanderthal-modern human hybrids fit the model I have suggested, while one-third were born to Neanderthal-modern human couples integrated into the mostly modern human tribe as modeled in the article, and that the long term couples collectively equally split between Neanderthal women and modern human men, and Neanderthal men and modern human women, then the effective percentage of Neanderthal contribution to the mtDNA gene pool would be not 25% but 2%, resulting in a much greater probability of losing Neanderthal mtDNA to random drift.

The Absence of Neanderthal Y-DNA in Modern Humans and Haldane's Rule

Needless to say, this model does not by itself resolve the absence of Neanderthal Y-DNA in modern humans, although its probability of loss to random drift would be on the order of the 52% estimated if the population was constant and Neanderthals contributed 25% to the total ancestry and there was a constant population.

But, here Haldane's rule comes into play and while the question of whether Neanderthals and modern humans were sufficiently genetically differentiated for Haldane's rule to apply was widely debated when this was first proposed, careful analysis of Neanderthal v. modern human Y-DNA and the pattern of autosomal Neanderthal DNA distribution across the human genome now strongly corroborates with direct evidence the hypothesis that Haldane's rule did indeed cause a disproportionate share of Neanderthal male-modern human female parent hybrids to be female and hence to lack Neanderthal Y-DNA.

Again, Haldane's rule doesn't have to operate with perfect efficiency to achieve the observed result with a high probability. 

If 80% of hybrid children were girls and 12% or less of the total ancestry is Neanderthal, then the probability of Y-DNA drift is equivalent to that of a randomly mating community with 4.8% Neanderthal ancestry, which makes the likelihood of loss of Neanderthal Y-DNA due to drift much, much higher than the 52% in a constant population model that you would expect in a community with 25% Neanderthal ancestry. If 90% of the hybrid children at girls, this falls to 2.4%, and both of those estimates are before considering the possibility that hybrid Neanderthal boys in a mostly modern human tribe may have had more of a selective fitness deficit than hybrid Neanderthal girls in a modern human tribe, which also seems quite plausible.

One can have very plausible parameters and end up with a very high probability of the loss of Neanderthal Y-DNA to random drift is some combination of a fairly effective Haldane's law, and greater selective fitness for hybrid girls relative to hybrid boys in modern human tribes for hybrids with a high percentage of Neanderthal admixture, are true.

In Nature, where Haldane's rule does apply, the preference for girls (in species with similar gender coding to primates) is much higher than 90%, so the estimates above are conservative. For example, male mules (i.e. horse and donkey hybrids) are "one in a million". A wide variety of studies across many species examined in a meta-analysis have demonstrated that the gender disfavored by Haldane's rule either doesn't happen at all, or produces sterile offspring, rather than fertile hybrid males being just significantly less likely than females (in primate-like sex determination schemes). For example, in a case of two species of primates in the same genus in the wild, Haldane's rule was found to apply to hybrid individuals:

Aguiar et al. (2008) studied species identity in groups of the howler monkeys Alouatta caraya and A. clamitans within their area of sympatry. They found that adult individuals of hybrid origin (on the basis of their mosaic coloration pattern) were almost always females. This led them to conclude that this (male-heterogametic) species adheres to HR.

There is not a consensus regarding the exact mechanism by which Haldane's rule operates, but it does tend to be an all or nothing affair except in extremely rare cases. 

Sex And Violence Go Together For Many Invertebrates

For humans, we often say that sex is a sign of commitment. But, octopi, insects and spiders are often really committed.

It’s not often that copulating octopuses eat one another—but it’s not uncommon either. “There just isn’t any way to measure how frequently it happens,” says David Scheel, a ecologist who studies octopuses at Alaska Pacific University. There are over 300 species of octopuses, and most are hard to study because they reclusively lurk in the depths of the ocean. Of these, a handful—including the giant pacific octopus—have been known to brutally murder and eat each other after sex. In 2014, researchers described (paywall) an instance in which a female octopus had sex with a male for 15 minutes, and then effectively strangled him with three of her tentacles by blocking his gills. 

But octopuses aren’t the only ones who kill their sex partners. Female praying mantises often kill their mates, especially if they’re hungry, and within certain species of spiders, the males will actually offer themselves as a meal for their newly-impregnated partners. 

Despite the ferocity of mating in the animal kingdom, romance is not dead: sexual cannibalism can be something of a gift from the male to the female in many cases. Female wolf spiders and tarantulas, who often eat males pre-intercourse, produce 30% more eggs than those who don’t when they finally get around to mating. And in the mantis’ case, the death of one male often means the survival of the reproducing female.

From here.

In the same vein, some fish, like salmon, while they aren't necessarily eaten by their partners, do make an epic journey to spawn and die when they finish.

I can't think of any terrestrial vertebrates that follow either pattern but would be happy to be corrected in the comments.

Was The Celtic Transition Demic?

Dental evidence supports I proposition that I have long argued for based upon other linguistic and historical evidence, i.e. that the Celtic linguistic and cultural transition, while pervasive, did not have much of a demic component. The gene pools of Celtic Europe changes much earlier in the late Neolithic and the early Bronze age, not during the Iron Age when the Celts appeared.

What the Celtic wave did was to reduce the evidence of the prior culture and language of the people in the regions that they came to rule to a mere substrate influence in Celtic culture, and largely confining those cultures to unattested pre-history.

Dental anthropological study of the proto-Celts, and continental and non-continental Celtic tribes during the Iron Age, particularly its applicability in estimating biological affinities of these tribes, has been generally overlooked. The present study helps fill the gap in the current understanding of these groups in several ways. First, 36 morphological traits in 125 dentitions from four regional samples, representing the proto-Celts, the continental and non-continental Celts, along with a comparative European Iron Age sample, were recorded and analyzed. Frequencies of occurrence for each dental and osseous nonmetric trait were recorded for each sample. Second, the suite of traits was then compared among samples using principal components analysis, (PCA), and the Mean Measure of Divergence (MMD) distance statistic. Multidimensional scaling and cluster analysis were subsequently employed on the triangular pairwise MMD distance matrix to graphically illustrate the relationships between samples. 

These biological distance estimates suggest the following: 1) dental phenetic heterogeneity is evident across samples, 2) the proto-Celtic sample does not show any evidence of population continuity with the continental Celtic sample, 3) there is a significant difference between continental and non-continental Celtic samples, and 4) there is a comparably significant difference among the Celtic, proto-Celtic and comparative samples. 

Simply put, the comparative results suggest that these groups represent biologically distinct populations. These findings were compared with published cultural, linguistic, genetic and bioarchaeological information to test for concordance between dental analysis and other lines of evidence. Several previous studies defined the Celts linguistically, using languages to link all the populations. The present study does not support these findings, and suggests there is more genetic diversity than previously assumed under this linguistic hypothesis. Thus, it appears that the transition from proto-Celtic to Celtic culture in these regions, and the subsequent spread of Celtic culture to Britain during the La Tène period, may have been primarily a cultural transition. The present study comprises the most comprehensive dental morphological analysis of the Celts to date, contributes to an improved understanding of Celtic tribal relationships and microevolution, and provides an initial impression of Celtic relationships to other European populations during the Iron Age.

This Dental Anthropology paper abstract is via the comments at the Eurogenes blog.

Private Sardinian mtDNA Halogroups Arose In Late Neolithic Through Bronze Age

The lion's share of mtDNA haplogroups in Sardinia are private to the island and derived from Neolithic mtDNA haplogroups. But, it took time in the pre-historic period for them to diversify. 

Some developed in the post-Nuragic period (i.e. post-Bronze Age Collapse ca. 1200 BCE), some developed in the Nuragic period ca. 1800 BCE to 1200 BCE. And some developed in the Chalcolithic period in Sardinia, which spans two archaeological cultures runs from about 2700 BCE to 2100 BCE, which was followed by the Bronze Age Bell Beaker culture prevailed until the Nuragic period, which may have been a later development and localization of the Bell Beaker culture (although apparently without a large demic component).

What was the Nuragic period named after? According to Wikipedia from the link above:

[N]uraghe, are megalithic towers with a truncated cone shape; they are widespread in the whole of Sardinia, about one nuraghe every three square kilometers. There has long been controversy among scholars. Theories about their utilization have included social, military, religious, astronomical role, as furnaces or sepulture places, but the modern agreement is that they were defensible homesites that included barns and silos. In ancient times, Greek historians and geographers tried to solve the mystery of the nuraghe and their builders. They described the presence of fabulous edifices, called daidaleia, from the name of Daedalus, who, after building his labyrinth in Crete, would have moved to Sicily and then to Sardinia. 

In the second half of the 2nd millennium BC, archaeological studies have proved the increasing size of the settlements built around some of these structures, which were often located at the summit of hills. Perhaps for protection reasons, new towers were added to the original ones, connected by walls provided with slits forming a complex nuraghe.

Nuraghe Santu Antine, Torralba, internal corridor 

It has been suggested that some of the current Sardinian villages trace their origin directly from Nuragic ones, including perhaps those containing the root Nur-/Nor- in their name (like Nurachi, Nuraminis, Nurri, Nurallao, Noragugume). Among the most famous of the numerous existing nuraghe, are the Su Nuraxi at Barumini, Santu Antine at Torralba, Nuraghe Losa at Abbasanta, Nuraghe Palmavera at Alghero, Nuraghe Genna Maria at Villanovaforru, Nuraghe Seruci at Gonnesa and Arrubiu at Orroli. 

Soon Sardinia, a land rich in mines, notably copper and lead, saw the construction of numerous furnaces for the production of alloys which were traded across the Mediterranean basin and nuragic people became skilled metal workers; they were among the main metal producers in Europe and with bronze they produced a wide variety of objects and new weapons as swords, daggers, axes, and after drills, pins, rings, bracelets, typical bronze statuettes, and the votive bronze boats that show a close relationship with the sea. 

Tin may have drawn Bronze Age traders from the Aegean where copper is available but tin for bronze-making is scarce; The first verifiable smelting slag has come to light, its appearance in a hoard of ancient tin confirms local smelting as well as casting. The usually cited tin sources and trade in ancient times are those in the Iberian Peninsula or from Cornwall. Markets included civilizations living in regions with poor metal resources, such as the Mycenaean civilization, Cyprus and Crete, as well as the Iberian peninsula, a fact that can explain the cultural similarities between them and the Nuraghe civilization and the presence in Nuragic sites of late Bronze Age Mycenaean, west and central Cretan and Cypriote ceramics, as well as locally made replicas, concentrated in half a dozen findspots that seem to have functioned as "gateway-communities."

The implication is that Sardinia must have been a pretty lawless and violent society (or had credible fears of regular raid attempts from outsiders) in the Nuragic period that made intense fortification of every village and hamlet necessary, centuries before Bronze Age collapse, and after the 4.2 kya climate event that was one of the most intensely arid periods in the West Eurasian region during the Holocene. In other words, they fortified themselves in an in between period that was a period of growth and consolidation of empires in most of the rest of Europe.

The paper and its citation are as follows: 

Sardinians are “outliers” in the European genetic landscape and, according to paleogenomic nuclear data, the closest to early European Neolithic farmers. To learn more about their genetic ancestry, we analyzed 3,491 modern and 21 ancient mitogenomes from Sardinia. We observed that 78.4% of modern mitogenomes cluster into 89 haplogroups that most likely arose in situ. For each Sardinian-Specific Haplogroup (SSH), we also identified the upstream node in the phylogeny, from which non-Sardinian mitogenomes radiate. This provided minimum and maximum time estimates for the presence of each SSH on the island. In agreement with demographic evidence, almost all SSHs coalesce in the post-Nuragic, Nuragic and Neolithic-Copper Age periods. For some rare SSHs, however, we could not dismiss the possibility that they might have been on the island prior to the Neolithic, a scenario that would be in agreement with archeological evidence of a Mesolithic occupation of Sardinia.

Olivieri et al., Mitogenome Diversity in Sardinians: a Genetic Window onto an Island's Past, Mol Biol Evol (February 8, 2017).

Hat Tip to Eurogenes.

Papuans Continued To Forage Long After Inventing Agriculture

In most places where agriculture was adopted, it replaced hunting and foraging. But, new hard evidence based upon isotypes in small mammal bones in Papua New Guinea demonstrates that there, foraging remained an important source of subsistence until at least 300 years ago. As a Science Daily press release explains:

In tropical New Guinea, where one of the earliest human experiments with agriculture occurred, agriculture apparently never replaced foraging as a primary subsistence strategy: "Montane tropical forest environments provided a stable source of subsistence for human hunter-gatherers in New Guinea," says Patrick Roberts, primary author of the study. "We have found out that foragers were living in close proximity to emerging farming groups, from 12,000 to 300 years ago, which indicates that agriculture was not a forced event in this part of the world." 

Tropical forests have frequently been perceived as unattractive habitats for humans -- both foragers and farmers -- due to poor soils, difficulties of humidity, and issues of reliable nutrition. However, archaeological work in New Guinea, among other tropical regions, has now helped to refute this idea: "We can now affirm that humans have occupied areas in this region, covered today in rainforest, from 45,000 years ago," says..., Professor Glenn Summerhayes from the University of Otago, senior author of the study. "Some of the earliest evidence for the human development of agriculture comes precisely from the tropical forested portions of New Guinea."

This is particularly notable, because most cultures in global history that have been slow adopters of agriculture have had a predominantly fishing based economy as an alternative, but in New Guinea we have a group of terrestrial hunter-gatherers in a tropical forest instead.

The abstract and citation to the source article are as follows:

The terminal Pleistocene/Holocene boundary (approximately 12–8 thousand years ago) represented a major ecological threshold for humans, both as a significant climate transition and due to the emergence of agriculture around this time. In the highlands of New Guinea, climatic and environmental changes across this period have been highlighted as potential drivers of one of the earliest domestication processes in the world. We present a terminal Pleistocene/Holocene palaeoenvironmental record (12–0 thousand years ago ) of carbon and oxygen isotopes in small mammal tooth enamel from the site of Kiowa. The results show that tropical highland forest and open mosaics, and the human subsistence focused on these environments, remained stable throughout the period in which agriculture emerged at nearby Kuk Swamp. This suggests the persistence of tropical forest foraging among highland New Guinea groups and highlights that agriculture in the region was not adopted as a unilinear or dramatic, forced event but was locally and historically contingent.

Patrick Roberts, Dylan Gaffney, Julia Lee-Thorp, and Glenn Summerhayes. "Persistent tropical foraging in the highlands of terminal Pleistocene/Holocene New Guinea." 1 Nature Ecology & Evolution 44 (2017).

Dravidian Speaking Gonds In India

The Central South Asian population known as the Gonds speak a Dravidian language outside and to the North of the main Dravidian linguistic area. From a population genetics standpoint, they look more like speakers of the Northern Munda Austro-Asiatic languages (derived from Southeast Asia) who experienced language shift at some point, and have little or no contribution of a component associated with Indo-Aryan migrants into India.

About The Irish Travellers

Irish Travellers are a linguistically distinct semi-nomadic population in Ireland with a lifestyle similar to the European Roma. But, a new genetic study of them has revealed that they are derived from the same population as the settled Irish and have no Roma genetic contribution.

They are as distinct genetically from the settled Irish as the Germans are from Italians or the English are from the Spanish, and there is some genetic substructure with at least two distinct populations and possibly three or four, that correspond fairly closely to linguistic differences.

Each of these sub-populations diverged from settled Irish populations genetically before the Great Famine in the mid-19th century. While other Irish populations have experienced exponential growth, Irish Travelers have suffered sustained demographic decline. The body of the paper says this about the divergence date between the settled Irish and the Irish Travellers.

The dating of the origin of the Irish Travellers is of considerable interest, but this is distinct from the origins of each population. We have estimated the point of divergence between the Traveller and the settled Irish population using two different methods. Our LD-based (TF) method estimates a split 40 (±2 std.err) generations ago, or 1200 (±60 – std.err) years ago (assuming a generation time of 30 years). Our IBD-based method (TIBD) estimates 12 (8–14) generations, or 360 (240–420) years ago. However both estimates suggest that the Irish Travellers split from the settled population at least 200 years ago. The Irish Great Famine (1845–1852) is often proposed as a/the source of the Irish Traveller population, but results presented here are not supportive of this particular interpretation.

The IBD based date is more reliable in this context as it controls better for issues related to having a small relatively genetically isolated population. So, that puts the divergence date around 1650 CE.

The paper's abstract and the citation for it are as follows:

The Irish Travellers are a population with a history of nomadism; consanguineous unions are common and they are socially isolated from the surrounding, ‘settled’ Irish people. Low-resolution genetic analysis suggests a common Irish origin between the settled and the Traveller populations. What is not known, however, is the extent of population structure within the Irish Travellers, the time of divergence from the general Irish population, or the extent of autozygosity. Using a sample of 50 Irish Travellers, 143 European Roma, 2232 settled Irish, 2039 British and 6255 European or world-wide individuals, we demonstrate evidence for population substructure within the Irish Traveller population, and estimate a time of divergence before the Great Famine of 1845–1852. We quantify the high levels of autozygosity, which are comparable to levels previously described in Orcadian 1st/2nd cousin offspring, and finally show the Irish Traveller population has no particular genetic links to the European Roma. The levels of autozygosity and distinct Irish origins have implications for disease mapping within Ireland, while the population structure and divergence inform on social history.

Edmund Gilbert, et al., "Genomic insights into the population structure and history of the Irish Travellers" 7 Scientific Reports 42187  (February 9 2017).