Wednesday, December 31, 2014

Jason's Golden Fleece ID'd

Greek mythology, like the Bible, is basically "legendary history".  It isn't all true, but it is grounded in historical events and places.  The most famous example, of course, is the historical existence of Troy and the Trojan Wars, although we can never know for sure if this war really involved a hollow wooden horse used to perpetrate treachery.

Recently, the Golden Fleece in the story of Jason and the Argonauts, has been identified with the Svaneti region on the Black Sea Coast of the Caucasian Republic of Georgia where sheepskins are used to collect gold flakes from eroding deposits in stream bed, much as they have in historically attested writings since 0 CE. It makes since, therefore, that this place could also have been the mythical part of the Colchis kingdom (also transliterated "Kolchis") on the Black Sea coast where the golden fleece myth originates from the Bronze Age Mycenean Greek people.

There are also remains of "warrior women" in Georgia, a bit further inland, correlated perhaps to the tale of the Amazons in roughly that region in the Argonauts story.

Interestingly, this would make sorceress and legendary tragic bad mother Medea ethnically Southern Caucasian, one of several points in the Argonaut story (another being the women of the island of Lemnos, which was one of the last to have a non-Indo-European language flourishing on it) where there is an interface between the pre-Greek and proto-Greek people (Jason had a Greek father and a pre-Greek mother).

Tuesday, December 30, 2014

Physical Constants Still Constant

A clever observation of some very dim stars confirms that the ratio of some key physical constants (the ratio of the proton mass to the electron mass) was the same 7.5 billion years ago as it is today. A similar result using essentially the same methodology carried out by a heavily overlapping set of investigators was obtained two years ago.  The universe is about 13.7-13.8 billion years old.

Now, neither of these constants are actually constant.  Both are functions of energy scale (as we know from the extreme conditions of colliders), but those energy scales were present in the universe only in the early parts of the first half-billion years of the universe.  But, some theories have supposed that there might be some other source of variation in these constants, a hypothesis that so far has no held up.

Saturday, December 27, 2014

Hunter-gatherers 7kya had stronger bones

Hunter-gatherers from 7,000 years ago had stronger bones than farmers from 1,000 years ago, probably due to the amount of strength building exercise they had.

In other news: archaeological traces of H. Erectus tools from 1.2 mya have been found in Turkey.

Eurogenes meanwhile has a refined thee autosomal population model of West Eurasians that suggests that Near Eastern Neolithic individuals probably has less Western European Hunter-Gatherer admixture than the Early European Farmer component derived from ancient DNA in the leading model of the kind.

Tuesday, December 23, 2014

Marnie On the Mesolithic-Neolithic Transition

Marnie at Linear Population Model has a series of well sourced posts on the Mesolithic-Neolithic transition.

The first examines the timelines of archaeological cultures in several areas in or near Europe with related commentary.

The next considers the geographic distribution of the "Early European Farmer" component of autosomal DNA in a three ancestral population analysis that peaks in Sardinia and is next most important in the Basque gene pool.

The third looks at the make up of modern Sweden as a mix of pre-existing European hunter-gatherers and early Swedish farmers.  Eurogenes, however, discounts this analysis as overly simplistic.

A particularly critical point that Marnie makes is that a fair share of what is viewed as a Neolithic contribution to the gene pool of Southern Europe may actually pre-date farming and be a Mesolithic legacy that arrived in the few thousand years between the end of the ice age and the arrival of herders and farmers.

OFF TOPIC: A cemetery with 1,000,000 mummies from ca. 500 CE has been discovered in Egypt, providing large numbers of non-elite body dispositions.  Some were buried as much as 75 feet under for some reason.

Monday, December 22, 2014

What's Up At Gambler's House?

Gambler's House had its sixth blog anniversary yesterday, and recently wrapped up a series of posts on the different lines of evidence regarding the origins and cultural affinities of cultures in the American Southwest.

This post is mainly just a list of the posts I’ve done in the “Tracing the Connections” series over the past few months. Here they are:


The Lay of the Land

The Evidence from Linguistic Relationships

The Evidence from Linguistic Contact

The Evidence from Oral Traditions

The Evidence from Skull Measurements

The Evidence from DNA: Introduction

The Evidence from DNA: Southwest-Specific

Overall, the evidence from all these different sources is very consistent in indicating that the modern Pueblos of New Mexico and Arizona are clearly the descendant communities of the ancient Pueblos in a general sense, but that tracing a line of descent between any specific ancient site and any specific modern Pueblo is not currently possible. With further research, however, I think there is a lot of potential for identifying more specific connections using multiple lines of evidence.

A winter solstice post, meanwhile, examined differences in building orientation that come in several macro-regional variations for reasons that aren't entirely clear.

Thursday, December 18, 2014

Latest Neutrino Mixing Parameter Data In, But Nothing Definitive

New Neutrino Physics Data

The latest neutrino physics data favors a normal mass hierarchy over an inverted mass hierarchy for neutrinos at a statistically insignificant 1.2 sigma level (roughly 2-1 odds in favor of normal v. inverted mass hierarchy).

The data favor a CP violation phase of 3/2pi (i.e. 270 degrees) but no CP violation is a possibility that is within the 90% confidence interval of the results.  Some earlier estimates of the CP violating parameter are here.

The new estimates of theta23 and of the difference in mass between the second and third neutrino mass states confirms prior estimates.

The new data also continue to constrain the parameter space of a fourth light neutrino species, which looks increasingly unlikely on a variety of fronts.

The Muon Anomalous Magnetic Moment

In other physics news, there is lots of work being done to refine the hadronic light by light contribution to the muon anomalous magnetic moment (aka "muon g-2"). While this is only one small part of about eight different sets of calculations that go into the final number, this part is the source of the lion's share of the uncertainty in the current theoretical prediction of this physical constant which is at a three sigma tension with the experimentally measured result.  There is a roughly 10% uncertainty in the hadronic light by light contribution to the muon anomalous magnetic moment, while many other contributions to the calculations (which make up most of the result) have uncertainties on the order of parts per million.

Despite this tension, in both absolute and percentage terms, the theoretical results and experimental result are both extremely close to each other.  The theoretical result has a current 0.5 parts per million uncertainty.  The experimental uncertainty is currently similar, but new measurements in the process of being made will bring the experimental uncertainty to 0.1 parts per million.  So, the odds are pretty good that the tension between theory and experiment that we are seeing right now arises because either the current theoretical estimate, or the current experimental measurement, or both, have understated margins of error.  It is hard to even devise a beyond the Standard Model theory that produces just the right amount of subtle discrepancy from the Standard Model theoretical prediction although many papers have been written trying to do so (usually in the context of SUSY models).

It could be that fixing the QCD uncertainty in the current theoretical estimate could produce a new theoretical prediction that could be reconciled with the experimental data, eliminating one or the more glaring tensions between theory and experiment in Standard Model physics and closing the door to many new Beyond the Standard Model possibilities.

As background, most of the calculations that go into determining the anomalous magnetic moment of the muon involve straight forward and extremely precisely known electroweak force factors.  But, there is some probability that a muon will decay into quarks and back, and determining the precisely impact of that possibility is very hard because the precision of QCD calculations is profoundly smaller than the precision of electric and weak force calculations (largely because quarks are confined making their low energy interactions impossible to measure directly).

Most of the recent work focuses on how to identify ways to find parts of the calculation that are exactly equivalent to specific measurable properties of bound mesons and baryons that can be substituted into the calculation which would otherwise have to be done from first principals, since we can measure the properties of bound hadrons with much greater precision than we can the properties of the quarks and gluons that are their components.

Meson Physics

The same conference proceedings that discuss the hadronic light by light calculations linked above also discusses experimental bounds on dark photons, and on a new fifth force that would act only on quarks.

The bounds on dark photons that interact with Standard Model particles are quite strict (something that disfavors a certain class of self-interacting dark matter models).

The bounds on a fifth leptophobic force with existing data show that any such force would have to be 100,000 times weaker than the strong force and 1000 times weaker than the electromagnetic force.  The relevant discussion also discusses how some targeted searches in new experiments, that would be little extra burden in experiments already planned, could tighten this only modestly model dependent bound considerably.

These bounds on a leptophobic fifth force are unexpectedly strict given the considerable uncertainties that exist in most quantitative applications of QCD - for example, we can only theoretically estimate the proton mass from first principals to an accuracy of about 1%.

Wednesday, December 17, 2014

Musing On The Y-DNA Of The First Farmers

The predominant Y-DNA haplogroup of the first farmers of Europe was Y-DNA haplogroup G2, together with some Y-DNA haplogroup I, the predominant Y-DNA haplogroup of European hunter-gathers (probably integrated into the farmer community from hunter-gatherers), and I believe, a bit of Y-DNA halogroup T.  This is consistent across the LBK farmers who were the first farmers of Central and Eastern Europe, the Cardial Pottery farmers who were the first farmers of Southern Europe, and the early Neolithic megalithic farmers of Western Europe.

Ancient DNA evidence strongly suggests that these first farmers replaced or demographically overwhelmed and assimilated in small percentages, the pre-existing hunter-gather men of Europe.

Relict populations, rich in Y-DNA haplogroup G, all of which likely date to this first wave of farmers, are found in several populations in the modern Caucasus mountains and Sardinia.  Y-DNA haplogroup G is also found at elevated levels in Corsica, Gascony (in Southern France), and Tuscany (which was home to the Etuscans of Italy before they suffered ethnocide within the Roman Empire).

Y-DNA haplogroup G has its greatest diversity in the Levant, which was part of the Fertile Crescent where farming was invented, suggesting that it originated there.  But, it is now most common in the Caucasus and the vicinity to the north of these mountains, where it is far less diverse.

Ancient DNA informs us that Y-DNA haplogroups R1a and R1b were almost entirely absent from the first farmers of Europe, appearing only in the Copper Age when they became the predominant Y-DNA haplogroups of Europe, diluting Y-DNA haplogroup G (and the small percentages of Y-DNA haplogroups I and T found in association with it) to low percentage frequencies in most of Europe.

Y-DNA R1b-V88, found mostly in Chadic people in Africa, arrived around 5700 BCE in the vicinity of Lake Chad, show signs of a linguistic connection to and wife taking from Cushitic people, probably in Southern Sudan.  But, Y-DNA R1b-V88 was not shared by any other African population to any great extent.

Y-DNA haplogroups J1 and J2 were also associated with early Neolithic peoples, although just how this played out is a bit unclear.  Today, J1 is confined largely to Semitic peoples who were traditionally herders in SW Asia.  Meanwhile J2 is associated with the highlands of the Fertile Crescent - Anatolia, the Caucasus, Armenia, and the Zargos Mountains, none of whom have ever been linguistically Semitic in attested history. There is a cline of relative J2 to J1 proportions from these highlands where J2 is more common, to the Bedouins of the Arabian desert, where J1 is predominant, but in most of SW Asia, there is a mix of both types in any given population.  Y-DNA haplogroup J is rare in North Africa and East Africa (and almost absent elsewhere in Africa).  Where it is found, Y-DNA J1 predominates.  Y-DNA J1 in East Africa is probably attributable mostly to Ethio-Semitic conquest ca. 1000 BCE, and in North Africa is probably mostly attributable to Islamic expansion and intercourse after 630 CE.  The genetic diversity of Y-DNA J is similar throughout Europe, West Asia and SW Asia, leaving a precise point of origin unclear.

The nearly complete absence of Y-DNA haplogroup J in the ancient DNA of the first farmers of Europe suggest that like Y-DNA R1a and R1b, that its presence outside SW Asia is due to a later migration wave.  It is also the case that outside SW Europe, Y-DNA J is predominantly Y-DNA J2, Y-DNA J1 in Europe is largely confined to Jews who migrated there in the historic era, and to areas where there was Muslim rule in the historic era.  The expansion of Y-DNA J2 into Europe may have been as a minor component of the initially Y-DNA R1a dominated expansion of the Indo-Europeans into Europe in second or subsequent waves of farmer and herder migration into Europe.

Europe was not the only receiver of the Fertile Crescent Neolithic package of farming, herding and other technologies and cultural traits.  The Fertile Crescent Neolithic package also spread to the Indus River Valley via diffusion at roughly the same rates seen in Europe across Iran, and to Egypt and beyond in North Africa.

Beyond these areas, the Fertile Crescent Neolithic package hit ecological and geographic barriers.  Fertile Crescent crops did not thrive in the climate of the African Sahel or Sub-Saharan Africa, and domesticated Fertile Crescent animals could not survive the tropical diseases of tropical Africa.  Fertile Crescent crops likewise were not suitable for the climate of tropical, monsoon driven Southern India.  The European and Central Asian steppe could support the herding of Fertile Crescent domesticated animals, but was too dry for the farm crops in the Fertile Crescent Neolithic package of the first farmers to thrive without inventing arid region optimized irrigation technologies (which eventually were invented).

The secondary centers of the Neolithic revolution that ultimately produced the Harappan civilization of the Indus River Valley, and the secondary center in Egyptian and North Africa, however, follow a very different demographic pattern than the demographic pattern observed in Europe.

In the Indus River Valley, prior to the arrival of Indo-Aryan invaders around 2000 BCE, Y-DNA haplogroups L and R2, as well as autochronous South Asian Y-DNA haplogroups like Y-DNA haplogroup H were common, while Y-DNA haplogroups R1, J2 and G that are predominant in early European and Near Eastern farmers were largely absent until the Indo-Aryans arrived in the wake of the collapse of Harappan society in the face of a severe climate event.  Y-DNA T is found in India, but largely in Dravidian areas of Southeastern India that did not adopt agriculture until around 2500 BCE using mostly African Sahel crops.  Y-DNA halpogroup T probably arrived in India at that time, and is otherwise largely absent from South Asia.

We don't know if Y-DNA L and R2 arrived in the Indus River Valley at the same time, or if they represent separate waves of migration to the region.  We do know that Y-DNA L is the sister clade to Y-DNA T and that the two clades may have geographically close origins to each other.  And, we do know that there are strong indications that the split of Y-DNA R into subclades R1 and R2 and possibly also into R1a and R1b, took place in Iran, which has maximal Y-DNA diversity today.  All Y-DNA R appears to have remote origins in the early Upper Paleolithic era in Southeast Asia and a very basal form of Y-DNA R was found in the ancient DNA of Ma'alta man from ca. 24,000 years ago in the Altai Mountain region at the far Southeast of the Eurasian steppe.

It is reasonable to hypothesize that the first farmers were Europe were from the Levant at the west end of the Fertile Crescent, while the first farmers of the Indus River Valley and Iran were from ethnically and genetically distinct populations probably originating from Mesopotamia and the Zargos Mountains at the east end of the Fertile Crescent (an area that in the Copper Age had thriving maritime trade with the Indus River Valley).

We also know that the Fertile Crescent Neolithic package involved several independent domestication events at different centers of population within the Fertile Crescent, that were then assembled into a comprehensive package, probably through trade and exchanges of small numbers of farming experts.  It was not invented by a single anthropological culture and the Fertile Crescent was rarely under the control of a single state or ruler in historic times.  So, it makes sense that different populations that developed particular components of the Fertile Crescent Neolithic package might have different population genetics.

In Egypt, which received the Neolithic revolution from the Fertile Crescent at about the same time as the Indus River Valley and the Balkans in Europe, there are traces of Y-DNA haplogroups G and T, but there is far more Y-DNA haplogroup T than there is Y-DNA haplogroup G.  But, there is very little Y-DNA haplogroup R1 in Egypt that is not traceable to the historic era. And the Y-DNA haplogroup E clades, typical of linguistically Afro-Asiatic areas that probably pre-date the Neolithic revolution are very common.  Thus, in Egypt, rather than the population replacement we see in Europe, we see a much milder demographic impact.  (King Tut was probably Y-DNA R1b, but that was likely attributable to the historic area Semitic Hyskos invasion and establishment of their Egyptian dynasties, or to Greek contacts with Egypt, not to the deep population genetic history of Egypt.)

This isn't to say that the Neolithic revolution didn't bring about immense demographic change in Egypt and North Africa.  Population densities increased by as much as a hundred-fold in a matter of a few centuries.  Any population that did not participate in the demographic population expansion that North Africa experienced as a result of the Neolithic revolution would be almost invisible in modern North African population genetics.

But, unlike Europe, the Neolithic Revolution in Egypt and North Africa was not largely a story of pure male population replacement by outside populations.  There is good evidence from the distribution and phylogeny of Y-DNA haplogroup E's subclades that it originated in the vicinity of Ethiopia, not in SW Asia as a back migrating clade.

Perhaps the fishing economy, and abundance of the hunting and gathering in the Nile Valley gave Egypt staying power in the face of Levantine Neolithic migrants in a way that was not true in Europe.  And, Egypt was the gateway through which all Neolithic expansion in Africa was filtered.

It is also possible, for example, that Y-DNA G and Y-DNA T may have represented two distinct populations in the Levant.  Perhaps Y-DNA G was made up of farmers and Y-DNA T was made up of herders.  In Europe, which was well suited to farming, Y-DNA G dominated, while Y-DNA T left a thin shadow of its range with much less demographic impact.

In contrast, in Egypt and beyond in North Africa and East Africa, herding was a much more significant component of the Neolithic revolution as there wasn't nearly as much arable land available to farm upon due to the narrowness of the Nile River Valley.  So, the impact of the Y-DNA T herder migrants from the Fertile Crescent may have been comparatively great and the impact of the Y-DNA G migrants from the Fertile Crescent may have been comparatively small.

Furthermore, historical evidence seems to suggest that it is much easier for people to transition from a terrestrial hunter-gather mode of subsistence to a herder mode of subsistence, than it is to transition from a terrestrial hunter-gather mode of subsistence to farming.  So, cultural transmission of the Neolithic revolution may have been easier in North Africa where that mostly involved teaching people how to be herders, than it was in Europe where that involved teaching people how to be farmers.  Hence, there may have been less economic pressure for the people who were the source of the Neolithic revolution to replace the existing population of North Africa than there was to replace the existing population in Europe (and probably also in Iran and Indus River Valley).

On the other hand, that specific scenario doesn't square very well with the fact that the Y-DNA T clades found in Southern Arabia are much younger than those in the Levant, or the fact that in SW Asia, low land herding is largely conducted by men who are Y-DNA J1 rather than Y-DNA T.

In general, the timing and circumstances by which Y-DNA J entered into its large demographic role in SW Asia, especially Y-DNA J1, is not clear.

UPDATED December 18, 2014 to correct numerous spelling, punctuation, grammar, and usage issues, as well as a few inadvertent errors, and to better spell out some incomplete thoughts.  Every once and a while when I'm in a really pinch for time, I come up with a real stinker in terms of formal writing errors like these.  I've also looked at Maju's comment and done a bit a research of Y-DNA J2 since this post, but I am not ready to see if I can add some substance to the discussion of Y-DNA J in this post.

Sunday, December 14, 2014

Quick Anthropology Hits


* Moroccan Berber men are overwhelmingly Y-DNA E1b1b1b-M81 and come from three main subhaplogroups within it, some more common than others. This Y-DNA haplogroup is rare outside Berbers and indicates a likely common and fairly recent origin for the Berber people, at least on the paternal line. This sheds light on the ongoing mystery of the exact relationship of the Berber languages to the other Afro-Asiatic languages and the ethnogenesis of the Berber people.

* Stripped of back migrating Eurasian DNA, the genetic diversity of Sub-Saharan Africa between populations is considerably less diverse than often assumed. African genetic diversity has more to do with its within population genetic diversity than it between population genetic diversity. Put another way, the "Black" component of Sub-Saharan Africans (as opposed to the Khoisan/Pygmy components) is fairly homogeneous across the continent. Of course, some of that is due to the relatively recent Bantu expansion.


* The raw Y-DNA data from the Caucasus reported here, seems to support a South of the "continental divide" in the Caucasus origin for Y-DNA R1b in Europe, probably sometime after Y-DNA G appeared there in a first farmer wave. The genetic evidence suggests that Southern Caucasian languages (like Kartevelian) might be a better place to look for links to the Vasconic and Minoan languages, than the North Caucasian languages.

* The lack of a proto-Indo-European word for tiger, a species that was present in all of these regions at the time, suggests a North of the Caucasus origin for Indo-European languages. This is also a death knell for an Out of India theory of PIE origins that would argue that Indo-European was a remnant of some dialect of the Harappan trade empire spoken at its fringes (perhaps in the BMAC area of Central Asia), since Harappan languages would have had a common word for Tiger. The strongest argument for Out of India had been the lack of any apparent substrate language in Rig Vedic Sanskrit.

* Bell Beaker blogger makes an intriguing case for a connection between the Indo-European words for witches and the possibility that old wise women may have been involved in brewing beer.

* Bell Beaker blogger has reviewed some recent research on Y-DNA R-1b (here and here) as well as mtDNA H. I still don't buy his North African Bell Beaker origins story, but the data and analysis are still useful. Eurogenes also speculates on R1b origins.

* A new Y-DNA tree shows how recent and extreme the expansions of R1b and R1a were compared to other Y-DNA haplogroups.

* New carbon dating data confounds the question of which archaeological culture was the source of the kurgan burial practice that is a litmus test for Indo-European affiliation in the leading theory of Indo-European origins. Yamnaya and Maykop kurgans now appear to have begun and evolved contemporaneously.

* Ancient DNA and DNA from his modern descedants has revealed were two instances of "false paternity" between King Richard III of England (whose bones were recently unearthed and confirmed in multiple ways) and his purported modern relatives. One was recent and distinguished one man who should have had the same Y-DNA type from the other modern relatives. The other was further back in history and suggests than none of the modern men who purport to come from the same paternal line as Richard III actually do, although it is impossible to tell just when the "false paternity" event took place.

* I discuss the outlier R1b hotspot in the Northern Ural Mountains in a comment at this blog about the Bashkirs. A neighboring, linguistically Uralic and not R1b rich people called the Udmurts are also notable outliers for their high frequency of red hair.

Planck Polarization Data Constrains Neutrino Physics

The Planck satellite measurements of polarization data in their cosmic background radiation data have been released.  In a nutshell:

* The margins of error in its measurements have been significantly reduced.  For a variety of reasons, moreover, these may be the most precise data points available for these physical constants for a long time.

* A low value for the Hubble constant remains.  This had been in tension with prior data but systemic errors in the prior data have been discovered that reduce that tension.

* A model with three rather than four light neutrinos is now favored at almost a five standard deviation level.  We know from particle physics experiments that there are at least three light neutrinos.  This rules out a fourth generation light neutrino or extra light sterile neutrino to explain a "reactor" anomaly which isn't looking like such an anomaly anymore anyway. This also tends to disfavor axions.

* The sum of the three neutrino masses is bounded to less than 160 meV at a 95% confidence level down from 230 meV after the first release of data. The best fit value is lower. The minimum value is about 100 meV in an inverted hierarchy of neutrino masses and about 59 meV in a "normal hierarchy" of neutrino masses. Thus, Planck still can't distinguish between the two scenarios, although science is getting very close to being able to do so. A degenerate neutrino hierarchy, where all three neutrino types have roughly equal masses has been ruled out.

Even though our knowledge of the absolute neutrino mass values isn't all that precise on a percentage basis (it is only slightly less precise than the accuracy with which we know the up and down quark masses), on an absolute magnitude of error basis (where the error range is +/- 50 meV), the neutrino masses are actually, by far, the most precisely known of the Standard Model fundamental fermion masses.

* There is still no data on primordial B-modes which the BICEP experiment proclaimed in tension with the old Planck data in a result that has been cast in doubt due to systemic error issues.  This should come in the next few weeks, however.  Thus, the question of the nature of cosmological inflation, if any, remains unresolved for the moment. Still, presentations like this one (see page 8) suggest that Planck will largely contradict and rule out the BICEP result, and greatly constrain inflation models to a narrow subset with little or no tensor component. The best fit is to a tensor mode r=0, and it is constrained to be less than r=0.09 v. BICEP's estimate of r=0.20.

Bottom line: The polarization data favors pretty much the most boring, most hostile to beyond the Standard Model physics result possible.  The very simple six parameter lamdaCDM model remains a very good fit to the data.

The results also greatly constrain thermal dark matter models. As I explained in a comment on the dark matter link (links added in this post to original comment which lacks links):
Thus, Planck seems to exclude entirely thermal relic warm dark matter with a WIMP-like annihilation cross-section.

Given the multiple problems with thermal relic cold dark matter with a WIMP-like annihilation cross-section pointed out by Warm Dark Matter proponents, the combined exclusion would seem to rule out all thermal relic dark matter with a WIMP-like annihilation cross section.

The lambda CDM model (which uses a definition of Cold Dark Matter that includes both thermal relic WDM and thermal relic CDM), requires a thermal relic.

So, if there is thermal relic dark matter it must not have weak force annihilation cross-sections and must instead be truly sterile with respect to the weak, strong and EM forces, although it might have self-interactions that do not lead to DM annihilation or at a different cross-section.

CDM in the absence of self-interaction doesn't seem to work at all to fit the galaxy scale data, so at this point you either have thermal relic WDM as keV scale sterile fermions that interact only via gravity and fermi contact forces, or there is no thermal relic DM at all. Such particles wouldn't be produced at the LHC or would be to light to detect in current direct dark matter detection experiments.

Other studies also place very strict bounds on purely bosonic DM (also here).

Axions escape this issue because it is not a thermal relic form of DM, but have other issues.

Of course, none of this rules out a fifth force or force modification approach.

Lyman alpha forest data from Planck seem to rule out WDM with particles less than 3.3 keV in mass which are too heavy to solve other CDM problems.

Thursday, December 4, 2014

More PMNS CP Violating Phase Numerology

A new paper by two Chinese investigators offers the conjecture that the CP violating phase of the PMNS matrix has a best fit estimated value of 39 degrees, with a range of 0 to 59 degrees.

The paper notes slightly broken symmetries in the CKM matrix that emerge when different parameterizations of its that produce almost identical CP violating phases are considered, and hypothesizes that these could be generalized to the PMNS matrix where the symmetries seem to be somewhat more strongly broken.

Tuesday, December 2, 2014

Lots of ancient mtDNA data from the American Southwest

The Gambler's House blog has a new post reviewing a large share of all published work on the subject (almost all of which is not open access and has vague abstracts that provide no substantive detail) with a wealth of New World ancient mtDNA information from the American Southwest, which other posts at the same blog have placed in archaeological, anthropological, and linguistic context.

The data cement the prevailing view that all Native Americans in the Southwest are descended either from a small founding population of the Americas ca. 14,000 years ago, or from a later Na-Dene migration wave (Navajo and Apache) that reached the American Southwest ca. 1,000 years ago.

The ancient mtDNA data also clarify that in several cases where it had not been clear that a change in archaeological culture corresponded to substantial demic replacement, that there was indeed a demic replacement (i.e. different groups of people arrived and replaced the people who practiced the old archaeological culture), and that two groups that were linguistically related despite substantial geographic separation where indeed genetically related.

The post also clarifies the genetic linkages of some groups in the American Southwest and with other Native American populations and provides some nice baseline data regarding how the founding mtDNA haplogroups of the Americas are distributed amongst various Native American populations.

I will try to expand further on the results and their context if I can find time to do so.

He also notes that ancient autosomal and Y-DNA data is unavailable at this time from samples in the American Southwest despite the availability of many scores of ancient mtDNA samples, and that there are only a small number of mtDNA studies that provide precision haplogroup subtypes beyond that available in the hypervariable region of mitochondrial DNA.

Wednesday, November 19, 2014

Two New Baryons Predicted By The Standard Model Discovered At LHC

The large hadron collider (LHC) has discovered two never before detected baryons (three quark composite structures in the same category as protons and neutrons), the Xi_b'- and Xi_b* 

The discovery is reported in a preprint here. The baryons have a bottom quark, a down quark and a strange quark each.  One has spin 1/2 and the other has spin 3/2.  The masses are essentially at the Standard Model predicted values.

A summary of the possible mesons and baryons in the Standard Model can be found at a previous post at this blog.  In the pertinent part that post noted that:
3. A chi baryon (isospin 1/2) (three horizontal lines) (J=1/2 or 3/2) have[sic] one light quark and two heavy quarks.

All four chi baryons without charm and bottom quarks, and all four chi baryons with one strange quark and one charm quark have been observed experimentally. Both of the J=1/2 bottom chi baryons and one of the two J=3/2 bottom chi baryons have been observed experimentally. One of the two J=1/2 double charmed chi baryon has also been observed.

Scientists have not yet observed one of the J=3/2 bottom chi baryons, one of the J=1/2 double charmed chi baryons, both of the J=3/2 double charmed baryons, any of the four of the charmed bottom chi baryons, or any of the four of the double bottom chi baryons.

Thus, exactly half of the twenty-four kinds of chi baryon ground states have been observed so far. In general, the baryons not yet observed are the heaviest ones.
This discovery involves the J=3/2 bottom chi baryon, and a first excited state of the J=1/2 bottom chi baryon above the ground state (the ground state of which has been observed already).  The double charmed chi baryons and the double bottom chi baryons remain to be observed, as do a variety of excited states.

Was mtDNA haplogroup H present in Mesolithic Iberia?

Today, the predominant mtDNA haplogroup in Europe is H.  It is absent from numerous ancient DNA samples everywhere to the north of the Olive Oil-Butter line in Europe before the advent of farming in Europe, and remains rare until the Copper Age that coincides with the advent of the Corded Ware culture in Central and Eastern Europe, and with the Bell Beaker culture of Western Europe.

There are a couple of studies, however, that claim to have found mtDNA haplogroup H in Iberia in the archaeological period immediately prior to the arrival of farming and herding there, sometimes called the Mesolithic era or Epipaleolithic era, that corresponds to the pre-Neolithic Holocene era.  There are quite early, but not as definitively Mesolithic, examples of mtDNA H in Italy and Southeastern Europe.  There is also mtDNA H in the early Neolithic Fertile Crescent (which is earlier in absolute dating than the Neolithic elsewhere).

The Iberian studies are the strongest evidence far mtDNA H having an origin in the Franco-Cantabrian refugia, as opposed to arising with the first farmers (and herders) or subsequent migrations that had run their course by the end of the Bronze Age in Europe (i.e. prior to 1200 BCE), or earlier.

Bell Beaker blogger challenges the validity of these studies in a pair of recent posts here and here.  He focuses on two points:

1.  The context of the ancient mtDNA H samples called Mesolithic is dubious, coming from old excavations of shell middens where samples were interspersed with Neolithic era pottery as well as older materials, and is also subject to other concerns related to its provenance.

2.  C14 dating of bone from people who had a shellfish heavy diet as the people buried in the shell middens that were a source for key ancient DNA samples are not reliable in the way that they are for terrestrial individuals.  Basically, their diet altered the baseline C14 levels upon which C14 data is premised from the standard assumptions concerning that baseline that are used to date the bones.

These criticisms, at a minimum, are not frivolous.  And, if these troublesome data points are excluded, in part on the intuition that extraordinary claims should require extraordinary evidence, then the rest of the ancient DNA data from Europe falls together into a much simpler picture.  In that picture, a much larger share of modern Europe's maternal genetic heritage arrived with the first farmers (or second wave of farmers), rather than dating back to integration of the continent's indigenous hunter-gatherer population into frontier farming communities (a more plausible possibility in the case of women than in men).  Bell Beaker blogger, in particular, doubts that mtDNA H could really have been so geographically confined for so long if it was really indigenous.

On the other hand, new autosomal DNA evidence seems to indicate that modern Europeans have fairly substantial genetic European hunter-gatherer ancestry.

I'm interested in hearing the opinions of others on these methodological critiques of this key evidence, upon which key conclusions about European prehistory and population genetics rests.

Tuesday, October 28, 2014

More Evidence Of Pre-Columbian Contact With Asia

In a recent post at this blog I recapped the evidence for pre-Columbian contact with the Americas after the Beringian land bridge was inundated. There were three main waves of subsequent migration:

* Saqqaq and Dorest Paleo-Eskimo populations are traceable to a wave of migration ca. 3500 BCE. These two archaeological cultures represent a single wave of demic migration and have genetic identity with each other (but admixed very little with other Native Americans before their demise).

* Early Na-Dene people arrive in Alaska ca. 1500 BCE.

* The 6th to 7th century CE Berginian Birnirk culture (in turn derived from Siberian populations) is the source of the proto-Inuit Thule people, who were the last substantial and sustained wave of pre-Columbian peoples to migrate to the Americas.

There were also several instances of less substantial and sustained migration, many of which have just become widely known:

* Around 1000 CE, Lief Erickson led a small population of Vikings to a short lived agricultural settlement called Vinland in maritime Canada. Recent discoveries announced in National Geographic in November of 2012 established that there were trade relations between the Vikings and indigeneous Arctic people at around the same time at the Northern tip of Canada's Baffin Island.

* From around 900 CE to 1100 CE, the "people who lived . . . in what today is the Lambayeque region, about 800 kilometers (500 miles) north of Lima, [Peru] had genetic links to the contemporaneous populations of Ecuador, Colombia, Siberia, Taiwan and to the Ainu people of northern Japan." These people were practitioners of the Middle Sican culture. It is not clear to what extent this contact was Austronesian in origin.

* I said then that:
Late in the period of Austronesian expansion (probably not earlier than 700 CE, with radiocarbon dated examples found in the Cook Islands by 1000 CE), perhaps from a final launching point at Easter Island, the kumara, a yam-like plant native to South America and possibly native to Peru, entered Austronesian territory and became a staple food. But, no genetic traces of the New World are found in Austronesian populations. It is possible that the kumara's arrival in Oceania and the Asian genetic influences found in Middle Sican graves involved the same instance of cultural Old World-New World contact.
The evidence now contradicts that contention insofar as it claims that there is no genetic evidence of Precolumbian contact in Polynesia. Razib Khan notes a new paper demonstrating that Easter Islanders have approximately 8% Native American admixture in their autosomal DNA arising from a Precolumbian admixture event. He notes that: "The rough dates for Amerindian ancestry admixture are in the range of 1300 to 1400 A.D., which match reasonably well with when Easter Island was settled."

* Razib also notes in the same post a new paper whose abstract states:
[W]e present 14C dates, and morphological, isotopic and genomic sequence data from two human skulls from the state of Minas Gerais, Brazil, part of one of the indigenous groups known as ‘Botocudos’. We find that their genomic ancestry is Polynesian, with no detectable Native American component. Radiocarbon analysis of the skulls shows that the individuals had died prior to the beginning of the 19th century. Our findings could either represent genomic evidence of Polynesians reaching South America during their Pacific expansion, or European-mediated transport.
As Razib sums up the finding of the paper in that post:
[H]eretofore the reasonable assumption about these Polynesian remains in interior Brazil were the product of escaped slaves, but there is an 80-90% probability that they died before any such enslavement of Polynesians could have occurred. In fact both remains may be pre-Columbian!
Both of the new papers appear in the most recent issue of the Journal Current Biology.

* Wikipedia summarizes many, but not all of these contacts, and adds others that I have not listed above.  Few are credible, but there is plausible evidence to support a few additional minor Old World-New World contacts.

* The Austronesians, the culture behind both of the latest two finds, are the same seafaring people who transplanted a community of their people from Indonesia, language intact, all of the way to Madagascar, with a small amount of South Asian admixture picked up along the way.

Of course, while these contacts did occur, none of them had the epic consequences that the era of European contact with the Americas begun by expedition of Christopher Columbus did.

New Insights From 45,000 Year Old Siberian Ancient DNA

A new study has the oldest modern human ancient DNA sequence every analyzed, from 45,000 in Siberia, assigned the name Ust’-Ishim.

Some key points:
The Y chromosome sequence of the Ust’-Ishim individual is . . . inferred to be ancestral to a group of related Y chromosomes (haplogroup K(xLT)) that occurs across Eurasia today. . . . The Ust’-Ishim mtDNA sequence falls at the root of a large group of related mtDNAs (the ‘R haplogroup’), which occurs today across Eurasia. . . . 
Based on genotyping data for 87 African and 108 non-African individuals, the Ust’-Ishim genome shares more alleles with non-Africans than with sub-Saharan Africans (|Z| = 41–89), consistent with the principal component analysis, mtDNA and Y chromosome results. . . . Among the non-Africans, the Ust’-Ishim genome shares more derived alleles with present-day people from East Asia than with present-day Europeans (|Z| = 2.1–6.4). . . . However, when an ~8,000-year-old genome from western Europe (La Braña) or a 24,000-year-old genome from Siberia (Mal’ta 1) were analysed, there is no evidence that the Ust’-Ishim genome shares more derived alleles with present-day East Asians than with these prehistoric individuals (|Z| < 2). This suggests that the population to which the Ust’-Ishim individual belonged diverged from the ancestors of present-day West Eurasian and East Eurasian populations before—or simultaneously with—their divergence from each other. The finding that the Ust’-Ishim individual is equally closely related to present-day Asians and to 8,000- to 24,000-year-old individuals from western Eurasia, but not to present-day Europeans, is compatible with the hypothesis that present-day Europeans derive some of their ancestry from a population that did not participate in the initial dispersals of modern humans into Europe and Asia.

Assuming that this corresponds to the number of mutations that have accumulated over around 45,000 years, we estimate a mutation rate of 0.43 × 10−9 per site per year (95% CI 0.38 × 10−9 to 0.49 × 10−9) that is consistent across all non-African genomes regardless of their coverage. This overall rate, as well as the relative rates inferred for different mutational classes (transversions, non-CpG transitions, and CpG transitions), is similar to the rate observed for de novo estimates from human pedigrees (~0.5 × 10−9 per site per year14, 15) and to the direct estimate of branch shortening. As discussed elsewhere, these rates are slower than those estimated using calibrations based on the fossil record and thus suggest older dates for the splits of modern human and archaic populations. [Ed. by Dienekes This is a very direct confirmation of the "slow" autosomal rate of ~1.2x10-8 mutations/generation/bp using a technology much different than those used before to estimate this. The slower mutation rate implies that major splits in human history (such as the Out-of-Africa event) took place much earlier than the Upper Paleolithic revolution and the spread of humans across Eurasia.] . . .

[W]e estimate that the admixture between the ancestors of the Ust’-Ishim individual and Neanderthals occurred approximately 50,000 to 60,000 years BP, which is close to the time of the major expansion of modern humans out of Africa and the Middle East.
In other words, this person lived just 5,000-15,000 years after Neanderthal admixture, a time which is on the recent end of other estimates of the timing of this event.

As a minor point, the discovery of 45,000 modern human remains in Siberia at all, provides a strong direct calibration point from which modern humans were known to be present at a specific out of Africa location.

Friday, October 17, 2014

Scalar and Tensor Dark Matter Doesn't Interact With SM Matter

All particles are either fermions, with total angular momentum J=0.5+N, or bosons, with total angular momentum J=0+N, in each case for N=0, 1, 2, 3 . . .  and the lower possible boson values for total angular momentum (aka "spin") have names.

spin-0 is called "scalar"
spin-1 is called "vector" and
spin-2 is called "tensor"

A recent measurement made by the ATLAS experiment at the Large Hadron Collider (LHC) set upper bounds on the cross-section of interaction between hypothetical scalar and tensor (i.e. spin-0 and spin-2) dark matter particles and the particles of the Standard Model.

These cross-sections of interaction can't be more than something on the order of 10-42 for scalar dark matter candidates with masses of between 1 GeV and 200 GeV+, and on the order of 10-40 for tensor dark matter candidates with masses of 1 GeV to 10 GeV, and as weak as 10-38 for dark matter candidates up to about 500 GeV. The LUX direct dark matter detection experiment imposes even stronger limitations on the cross-section of interaction of scalar dark matter candidates with masses of 10 GeV to 200 GeV+ of less than 10-44.

Furthermore, multiple lines of observational evidence strongly disfavor "cold dark matter" models.  Models with particles with more than 200 GeV masses are particularly strongly disfavored.

Thus, any scalar or tensor dark matter candidates must have interactions with ordinary matter than are many order of magnitude weaker than the slight interactions of neutrinos with other forms of ordinary matter.

Realistically, if scalar or tensor dark matter exists at all, it doesn't interact at all with particles outside the dark sector.  In all likelihood, they simply don't exist at all, because if they interacted with other dark matter particles that had higher cross-sections of interaction, you would at least see indirect evidence of their existence as they couple to other forms of dark matter with higher cross-sections of interaction with the Standard Model.

Now, in fairness, almost nobody in the astronomy community is seriously proposing massive scalar or tensor dark matter candidates, and in the most popular models that have a boson in the dark sector, self-interacting cold dark matter models, the typical candidate, sometimes called a "dark photon" is a vector boson (i.e. spin-1) with a mass of around 100 MeV (about ten times lighter than the low end of the scale proposed by ATLAS in this experiment).

So, while this ATLAS result ruled out one subtype of conceivable dark matter, it didn't do much to rule out the leading contenders in the race to explain dark matter phenomena (e.g., light axion dark matter, keV mass scale sterile neutrino-like fermionic dark matter, and GeV mass scale fermionic dark matter such as gravitinos and the fermion partners of Standard Model bosons in SUSY theories).

But, this is a blow to SUSY, because minimal SUSY theories create a myriad of new massive scalar particles, the lightest of which are good dark matter candidates, and some non-minimal SUSY theories often also create new massive tensor particles.

In particular, all R-parity conserving SUSY theories should have one or more massive scalar dark matter candidates, and R-parity violating SUSY theories are hard pressed to explain why SUSY dark matter still exists.  In R-parity violating SUSY models, one has to manipulate the SUSY model to prevent thermal relic, R-parity violating SUSY dark matter from all decaying to Standard Model particles over the life of the universe, something inconsistent with dark matter observations from astronomy.

META OBSERVATION:  Since the Dispatches at Turtle Island blog was created, there have been 101 posts including this one, that address the issue of dark matter to some extent (about 15% of all of the posts at this blog).  This is appropriate because dark matter is the most obvious and practically relevant of the unsolved problem in physics.

Tuesday, October 14, 2014

DM Halo Surface Density Not Universal After All

A new review finds that that the surface density of inferred dark matter halos is not universal as previously concluded in other studies.

There is also a new high precision inference of dark matter distributions in a set of colliding galactic clusters.

The Latest Lattice QCD Quark and Meson Mass Conclusions

Using the physical masses of Ds, Ds and J/ψ as inputs, Sommer's scale parameter r0 ... the masses of charm quark and strange quark in the MS scheme are determined to be r0=0.458(11)(8) fm, mMSc(2GeV)=1.111(12)(22) GeV (or mMSc(mc) = 1.291(10)(18) GeV), and mMSs(2GeV)=0.103(6)(8)GeV, respectively. Furthermore, we observe that the mass difference of the vector meson and the pseudoscalar meson with the same valence quark contents is proportional to the reciprocal of the square root of the valence quark masses.
From here.

These results are consistent with (at a 1 sigma level), but at the high end of, existing global average experimental values, and other recent lattice QCD calculations, although neither of the new estimates is record setting in its precision.

The pole mass of the charm quark is 1.291(21) GeV, compared to the value of PDG 1.275(25) GeV. Another recent lattice QCD analysis claimed that the charm quark mass was 1.273(6) GeV.

The strange quark mass (for which the pole mass is ill defined) is 0.103(10) GeV, compared to the PDG value of 0.095(5) GeV. Most strange quark mass estimates are below the mass of the muon, which is 0.1056583715(35) GeV, but it is not entirely certain that the mass of the muon is greater than (or different from) the appropriately defined mass of the strange quark. Two other recent lattice QCD determinations of the strange quark mass came up with 0.094(9) GeV and 0.992(39) GeV, respectively.

The relationship discussed between vector meson (i.e. spin-1 odd parity mesons) masses and pseudoscalar meson (i.e. spin-0 odd parity) masses in bold in the quoted material above appears to be a novel observation. I will have to read the paper more closely to clarify if this is merely an empirical observation or exists for some deeper reason.

There are two other grounds states of mesons - pseudovector aka axial vector mesons (i.e. spin-1 even parity), and scalar mesons (i.e. spin-0 even parity) that do not readily fit simple quark models of mesons.

Meanwhile, the final combined top quark mass measurement from Fermilab including all data through its shutdown from both experiments is 174.34(64) GeV.

Monday, October 13, 2014

Columbus Day

The line between pre-Columbian and post-Columbian history in the New World is October 12, 1492 CE (using the calendar conventions of the time that have shifted a bit since then), the day the Christopher Columbus and his small fleet arrived in the Americas after the maritime trip from Spain, financed by Queen Isabelle, across the Atlantic Ocean.  This set off a cascade of dramatic events in the Americas that have forever changed these two continents.

The year is also notable because in this year, the Reconquista was completed and the Muslim Moors were expelled from their last redoubt in Southern Iberia.

The Renaissance was in full swing at this point.  The Protestant Reformation's beginning is conventionally dated to 1517 CE.  In England, Queen Elizabeth I would go on to take the throne on November 17, 1558 and her fleet's defeat of the Spanish Armada, thirty years later, in 1588, would stun Europe.

This is recognized as "Columbus Day" by the federal government in the United States, and many other governmental entities in the U.S. and elsewhere in the Americas (observed this year on Monday, October 13, 2014 by the federal government since October 12, 2014 is a Sunday).

The modern significance and politics of this holiday in the United States is beyond the scope of this blog.  But, this event itself continues to be arguably the most significant one in the history of the Americas.

Friday, October 10, 2014

More Problems With Dark Matter

In a new preprint by Wu and Kroupa of October 8, 2014, accepted for publication in MNRAS and entitled "Galactic rotation curves, the baryon-to-dark-halo-mass relation and space-time scale invariance" these advocates for MOND and related theories in lieu of dark matter raise multiple new serious concerns about both cold dark matter and warm dark matter theories.  They also use statistical methods applied to large sets of galactic rotation curve fits to determine which of the MOND interpolation formulas is more accurate.

The highlights:

* Empirically, the fit of galactic rotation curves to baryonic mass distributions is much more tight than in the galaxies produced by CDM and WDM simulations, despite the fact that the observational evidence has measurement errors which are absent in the simulation data.

The "standard" interpolation function in MOND models outperforms the "simplified" version, although both are very good fits.  The WDM model has about twice as much scatter as the "simplified" MOND theoretical prediction line.  The "tamed" CDM models that make unphysical assumptions to replicate reality are twice as bad as WDM simulations.  And, the fully realistic CDM models have massive scatter despite the fact that the real world galaxies behave almost precisely as the standard interpolation function from MOND predicts.

A non-parameteric statistical test disfavors all of the CDM and WDM models and the simple MOND model when compared to the observational evidence by 99.99%, while finding it 80%-90% likely that "standard" MOND and another sophisticated MOND variant called SID are a fit to the data.  This is particularly stunning given the amount of measurement error involved.

The link between baryonic matter distributions and apparent dark matter halo distributions is so tight with such a simple formula that it is very hard to see how any DM theory could achieve this result.  The "scatter" of different possible dark mater halos for given baryonic matter distributions in DM theories are fundamental, built in, parts of the theory.

* All DM model simulations systemically over predict the amount of dark matter in galaxies of a given baryonic mass, while the amount of dark matter that would be necessary to reproduce the MOND results is right on the money.

* Kroupa acknowledges to important facts that one has to correct for when using MOND to predict galaxy dynamics: (1) the non-luminous interstellar gas to star mass ratio, and (2) the impact of fields from nearby objects (e.g. the impact of gravity from a central galaxy on the dynamics of a satellite galaxy) aka the "external field effect".

In general, more non-luminous interstellar gas simply requires an adjustment in the estimated amount of ordinary baryonic matter in a system.

Outside gravitational fields, in general, reduce the apparent amount of dark matter in the system in the eyes of a Newtonian observer.

Bonus trick:  If you know the amount of luminous matter and interstellar gas in a system, and how fast it is rotating, you can use this slightly more sophisticated version of MOND to determine how far the influenced gravitational system is from the outside object created gravitational system.

* Dark matter halos inferred by Newtonian observers when MOND is used to govern dynamics have the correct isothermal shape the observational evidence implies, rather than the NFW distribution that CDM models naturally produce.

* About 70% of disk galaxies are "bulgeless" and MOND can easily reproduce these dynamics in the face of various galaxy formation scenarios.  But, WDM and CDM models create far, far too few bulgeless galaxies, because those models tend to create serious bulges whenever DM halos or galaxies merge, which happens a lot.  Some WDM/CDM simulations cheat to prevent relatively equal galaxy collisions like the Bullet cluster and get results more like real life, but there is no physical mechanism to cause that to happen and we know that big collisions are far more common than the "tame" simulations permit.

* These very accurate results are achieved with the usual one MOND parameter (plus external field effects and gas-star mass ratios in particular galaxies), and very easy math compared to many competing theories.

* It sounds like some progress has been made in physically motivating the equations and in reducing the amount by which apparent DM is underestimated at cluster scales from the "old days" although these continue to be problems.

I'll admit that I've definitely flirted with WDM models, which are definitely closer to observational evidence than CDM models that perform just dismally.  But, this analysis makes it extremely hard to believe that there are really any dark matter particles out there at all.

Tuesday, October 7, 2014

Tracing The Genetic Roots Of Western Europe With Megalithic Ancient DNA


Today, the predominant Y-DNA haplogroup of Western Europe (and a fair amount of Northern Europe), inherited via patrilines, is R1b, and the predominant mtDNA haplogroup in Europe, which is inherited from one's matrilineal ancestor, is H. The question, which turns out to be fairly hard to answer, is when Europe's current population genetics took their current form.

If you know when this happened, then the already well developed archaeological history of Europe can point you to the archaeological culture that appeared when the last major demic migration in history shaped the gene pool of Western Europe.

Western and Northern Europe were depopulated during the Last Glacial Maximum (ca. 20,000 years ago) outside two Western European refuges of hunter-gather people, the Franco-Cantabrian refuge, and Italian Penninsula (there was another refuge in the Caucasus  region).  This was followed by the repopulation of Europe during the Mesolithic era (early Holocene ca. 8,000 BCE), followed by the first wave Neolithic revolution (in most of Western Europe, the megalithic culture ca. 5000-3000 BCE), then the Bell Beaker culture and cultures derived from it (ca. 2900-1200 BCE), and then Celtic and Germanic Indo-European cultures (ca. 1300 BCE) which persisted until the expansion of the Roman Empire as far as Iberia, France and England.

If you know which of these archaeological culture was responsible, you are much further along in answering an even deeper and more primal question:
Who are the deep prehistoric ancestors of Western Europeans who are themselves the ancestors of most European-Americans.
Astonishingly, in the last few years, it has been possible to come up with some pretty solid answers to these questions by comparing the DNA left behalf by members of archaeological cultures are various time depths from many thousands of years ago, and comparing them to contemporary populations.

Once the preliminaries are out of the way, this post will focus on trying to determine if the modern gene pool of Western Europe mostly took shape as part of the Atlantic Megalithic culture, which is an undersampled community of first farmers and first herders in this part of Europe who raised monuments like Stonehenge. This was the most intense demographic event of the last few thousand years in Europe, so it is a natural place to look.

But, it could have happened earlier, with current European population genetics resembling that of the Western European hunters and gathers who roamed Europe before the first farmers arrived, who have made a major autosomal genetic contribution (probably more than a third of autosomal ancestry) to the modern Western European gene pool.[1]

Or, it could have happened later, in the Copper Age and Bronze Age, perhaps, even later, in the wake of Bronze Age collapse and the advent of the Iron Age.

What We Know About Ancient DNA In Various Archaeological Cultures

We know from a variety of ancient DNA sources that Y-DNA I2 and mtDNA U were predominant in much of Europe in the Mesolithic, although it isn't entirely clear that the far Atlantic coast region is fully typical of this trend.[2]

There may be mtDNA V in the Atlantic Mesolithic as well. Today mtDNA V is found among Berbers, the Saami of Finland, coastal Atlantic populations and people in or near Basque Country. There are some indications of mtDNA H and HV in Iberia and/or the Italian refugia in the Mesolithic as well.

 This suggests that this common genetic affinity arose from a dispersal sometime before these populations acquired languages from four different language megafamilies (Uralic, Indo-European, Basque and Afro-Asiatic), although the are competing theories about its origins.[3][4]

But, these linguistic limitations aren't necessarily all that powerful given the likelihood that the Uralic language was adopted by the Saami around 1500 BCE, that Indo-European languages arrived in the coastal Atlantic area ca. 800 BCE, that the Vasconic languages probably arrived in Europe ca. 2900 BCE, and that the time at which the Berber's adopted their language is not well established but could have been as recent as the domestication of the camel (camels were domesticated in Arabia ca. 3000 BCE, but were present in the Levant and in North Africa where Berber languages are spoken only ca. 1000 BCE - 900 BCE).

The high frequency of mtDNA V in the Saami favors a founders effect in this population in the Mesolithic era, but one can't rule out a source, for example, from the including of Finland all of the way up to places north of the Arctic Circle (when a rapid expansion of the Saami population as a result of its adoption of food production technology from the Indo-European Corded Ware Neolithic culture that preceded their adoption of a Uralic language could make it possible for founder effects from the people who integrated Saami hunter-gatherers into their herding and farming communities at the time to greatly influence the post-expansion gene pool. The Saami integration of mtDNA V into its gene pool could have been independent, but roughly contemporaneous with a source of mtDNA V in all of the other locations where it is found, perhaps as a much lower frequency component of the mtDNA mix of an initial Bell Beaker population which had a much larger effective, than the percentage of the founding Neolithic population that merged with the pre-Saami, which might have had a much smaller effective population size size than the Bell Beaker people.

The first wave Neolithic in most of Europe is Y-DNA G2a and a mix of mtDNA types with less mtDNA H than there is now.[2][5] But see [6] (reporting continuity between Neolithic mtDNA from Northeast Spain ca. 3500 BCE and modern Iberian mtDNA, in contrast to the results in LBK samples of [5] from ca. 5500 BCE). First wave Neolithic populations everywhere crashed after a population bubble and there was a significant population rebound at some point after this crash which is a likely source of the post-first wave Neolithic, pre-Iron Age shift in European population genetics.[7]

The only ancient DNA from Bell Beaker, from Central Europe, has the Y-DNA R1b and mtDNA H at high levels that is the typical of Western Europe.[8] But, this is just a single sample at the fringe of the Bell Beaker area.  It is also equally consistent with an Atlantic megalithic or Mesolithic source for Y-DNA R1b in Europe that was present on a continuous basis since those time and into the Bell Beaker era.  Indeed, conventional assumptions based on archaeology about the demic impact of the Bell Beaker people on the places they came to settle would have expected just this kind of continuity.

But, as we will see later in this post, despite the existence of dozens of ancient Y-DNA samples from early Neolithic and Mesolithic individuals in the territory where the Bell Beaker culture or its cultural successors extended, there is not a single instance where a Y-DNA R1b individual has been identified.  Not in European hunter-gatherer populations (where Y-DNA I2 is predominant), not in LBK or Cardial Pottery Neolithic populations including Southern France and Spain  (where Y-DNA G2 is predominant).  A specifically identified ancient mtDNA sample from an Atlantic megalithic site further North in France, likewise has a mix of halogroups much more consistent with other first wave Neolithic sites than with the mix in the Bell Beaker era and at all subsequent times.

Ancient DNA evidence establishes that the predominant source of R1a and mtDNA H in Central and Eastern Europe is almost certainly the Corded Ware culture that followed the collapse of the first wave Neolithic archaeological cultures, such as the Linear Pottery aka LBK culture, and its successors, in the region.[9][10]

Interestingly, there there is great affinity between sea faring, non-Indo-European, Minoan's of Crete who incorporated contests with bulls into their culture and modern Western European populations in both Y-DNA and mtDNA).[11][12] These links and the fact that the Bell Beaker and Minoan civilizations were roughly contemporaneous suggest that they could have a connection, although the material culture connections between the two cultures isn't necessarily all that compelling.

Minoan Crete, in turn, shows stronger ancient DNA genetic ties to Anatolia than to the Balkans (which is the area with more of an affinity for the remainder of Greece).[13] But, this was not always the case. A review of 15 ancient mtDNA samples from 8000 BCE at the dawn of the Fertile Crescent Neolithic favor a migration route of the first wave of farmers from the Fertile Crescent into Europe via Cyprus, Crete and the Aegean rather than Anatolia.[14]

The population genetic impact of Indo-Europeans in Western Europe was probably modest. I estimate that the impact was probably on the order of 5%-15%,

This is based upon taking the Basque population as representative of the Northern Iberian population immediately prior to the arrival of the Indo-Europeans, and then looking at the haplogroups found in areas that subsequently became Celtic (which were probably Vasconic before the arrival of the Celts), but are not found in Basque populations, as an order of magnitude estimate of the Indo-European population genetic impact, since population genetics in Western Europe have been largely stable since the Indo-Europeans arrived in Western Europe.

The fact that the two populations aren't all that different, even though they are somewhat distinct, suggests that the Indo-Europeans who arrived in Western Europe predominantly in the Iron Age, had a quite modest impact on the region's gene pool.

Contemporary Population Genetics

These days, the most basal forms of Y-DNA R1b are found in Iran [15], the eastern Caucasus [16], Armenia [17], and Turkey[18]. So, ultimately, it seems very likely that Western Europeans can trace their roots to a migration sometime during the Holocene area (i.e. that last 10,000 years) from the highlands of West Asia.

Y-DNA R1a, the dominant Y-DNA haplogroup in the rest of Europe which expanded to become common where it is found today at approximately the same time as the R1b expansion, also probably originates in eastern Turkey or Iran,[19]

Linguistic Conjectures

Geographically, this region where R1b orignated corresponds fairly closely to the geographic range of the copper age Kura-Araxes culture (ca. 3400 BCE to 2700-2000 BCE)[20][21] which archaeological evidence demonstrates had longstanding and sustained trade ties (at least) to the Sumerian Uruk culture (ca. 4000 BCE to 3100 BCE).[22] It isn't clear to what extent the Kura-Araxes culture's metal working technologies derived from the Sumerians who neighbored it to the South, or the Maikop culture, who were its Northern neighbors.

The Kura-Araxes culture probably spoke a language belonging to the now extinct the Hurro-Urartian language family.[23] Linguistic overlaps between the Hurro-Uratian and Sumerian languages, which are statistically significant at approximately the p=0.02 level, suggest that the languages are related to each other in some way.[23] But, the words that they have in common are not a good fit to either borrowing of loan words, or to a model in which both languages share of proto-language.[23] Instead, it seems likely that either a Hurro-Uratian population was in the process of adopting a Sumerian superstrate language which was aborted before it could run its course, or that alternately, a Sumerian population was in the process of adopting of Hurro-Uratian superstrate language and that process was aborted before it was completed, as the pattern of shared words is similar to the small number of cases where that scenario is attested.[23]

Hurrian was spoken in Mesopotamia, and eastern and southern Anatolia ca. 2200 BCE to 1000 BCE. The language of the Kassite people (ca. 1500 BCE to 1100 BCE) in an area that overlaps heavily with the region of the Kura-Araxes culture's extent, was probably also a part of the Hurro-Uratian language family.[24]  Uratian which is widely acknowledge to share a language family with Hurrian was spoken in what is now eastern Turkey and modern Armenia at least between 900 BCE and 600 BCE.  The strongest candidate for a modern family of living languages related to Hurro-Uratian is the Northeast Caucasian language family.

Thus, Minoan civilization may have been the result of an intrusive Copper Age Anatolian population's migration to the island, perhaps related to the non-Indo-European Hattic culture that preceded the Indo-European Hittite civilization that began its conquest of Anatolia and the northern Fertile Crescent at a historically attested date after 2000 BCE, in the wake of the highly disruptive 4.2 kiloyear climate event that was also probably pivotal in the fall of the Sumerian language to the Semitic Akkadian language in Mesopotamia.

The Hattic language shows similarities to the Northwest Caucasian and South Caucasian languages, and to the thinly attested languages of the Kaskians of northeastern Bronze Age Anatolia, in the mountains along the Black Sea coast, who may be the ancestors of the Northwest Caucasian Circassian people today. This language family is also a likely candidate for the language of the Maikop culture.

Proposals to link the Northeastern and Northwestern Caucasian languages into a North Caucasian language family have received serious consideration, and if well founded, would link almost all of the non-Indo-European languages of the Copper Age region in which Y-DNA R1a and R1b in Europe both have their likely origins into one linguistic family that probably also would include the Basque language and Minoan.

Minoan may also have been part of the same language family as the non-Indo-European substrate language of Greek, and of other known non-Indo-European languages of the Aegean and Italy such as Lemnian (spoken through about 600 BCE on the island of Lemnos near the Anatolian coast in the Aegean sea that was annexed to Greece in 1912, the Etruscan language spoken in early Roman times (through about 0 CE) in what is now Tuscany, and the Raetic language of the Italian-Austrian Alps that was part of the same language family as Etruscan and survived somewhat longer (no relation to the Indo-European language of the same name now spoken in Switzerland).

Y-DNA R1a, the dominant Y-DNA haplogroup in the rest of Europe which expanded to become common where it is found today at approximately the same time as the R1b expansion, also originated to the north of the historically attested copper age Elamite civilization of Iran and the contemporaneous Sumerian culture of Mesopotamia.[19]

This would put it in the vicinity of both the Kura-Araxes culture and the Maikop culture (aka Maykop culture) (ca. 3700 BCE-3000 BCE) immediately to the north of the Kura-Araxes culture in the Northern Caucasus mountains. The Maikop culture, under cultural influences from Iran and South Central Asia developed metal working technology independently of the Sumerians or the Balkan-Anatolian copper age cultures.[22] The Maikop culture also invented the Kurgan burial practices that would later spread (along with its metal working technology) to the probably proto-Indo-European Yamna culture of the Pontic Steppe (ca. 3500 BCE to 2200 BCE) where these burial practices would become the litmus test for Indo-European cultural affinities.[25] The Maikop culture itself, however, may very well not have been Indo-European linguistically.

But, can be do better to pin down the time and place of the predominant genetic ancestors of Western Europeans?

The Big Open Questions

The source of Y-DNA R1a and mtDNA H in Central and Eastern Europe was very likely the Indo-European Corded Ware culture, not so far from an Indo-European homeland on the Pontic Caspian Steppe whose antecedents started to gel around 4000 BCE.

The predominant source of Y-DNA R1b and mtDNA H in Western Europe is more controversial.

1. Does R1b originate in the Paleolithic hunter-gatherers from the Franco-Cantrabrian refugium or Northwest Africa? This hypothesis was advanced, for example, in a 2013 paper.[26]

2. Does R1b have its source in the first wave megalithic Neolithic?  This is not true in the case of other first wave Neolithic populations in Europe, whose closest match among modern populations are the people of the island of Sardinia whose ancient DNA and physical anthropology show continuity from Neolithic times to the present.[1][27][28]

3. Does it come after them, with the Bell Beaker culture and its immediate successors of the Copper Age and early Bronze Age?

4. Does it come with the late Bronze Age/early Iron Age Indo-European Celts?

5. Or, does this happen when later ruling powers like the Romans (whose Italic family language is also Indo-European and closely related to Celtic), arrive.

Increasingly, it is my view that the answer is choice number 3.  Western European ancient DNA starts to look very modern from this point onward, but the hints we have gotten about the genetics of the Atlantic megalithic culture appears to resemble other first wave Neolithic cultures (whose genetics are quite distinct from modern Europeans) rather than modern Western Europeans.

Did Y-DNA R1b and mtDNA H Become Common In The Megalithic Era Or Metal Age Age In Western Europe?

If Y-DNA R1b and mtDNA H either expanded in the Mesolithic and was incorporated heavily into the first wave Neolithic culture of the Atlantic megalithic culture, or if the Atlantic megalithic culture, rather than later metal age cultures in Western Europe, were the source of Y-DNA R1b and mtDNA H in Europe, then the population genetics of the Atlantic megalithic people should be significantly different from first wave Neolithic populations in Central and Eastern Europe (LBK) and Southern Coastal Europe (Cardium Pottery).

If Y-DNA R1b and mtDNA H are scarce or absent in Atlantic megalithic ancient DNA, in contrast, then there has to be a major metal age migration of people that is the source of these population genetic components in Western Europe, and this increasingly looks like it must be Bell Beaker and associated cultures, which were probably linguistically Vasconic (i.e. part of the language family that includes Basque and some extinct Iberian languages), because if Indo-Europeans were the source of these genetic components, the pre-Indo-European Basque people would not be extremely high in Y-DNA R1b and mtDNA H.

Fortunately, in the last few years, some ancient Atlantic megalithic ancient DNA samples have been sequences allowing us to finally make progress towards answering some of these questions.

As set forth in detail below, the limited available data is consistent with the Atlantic megalithic culture being a first wave Neolithic culture that is very similar to that of first wave Neolithic cultures elsewhere in Europe from a population genetic perspective, and is inconsistent to the extent that we have data, with the Atlantic megalithic culture being the main source of Y-DNA R1b and mtDNA H in modern Western Europe.

In contrast, the limited data that is available is consistent with Y-DNA R1b and mtDNA H being spread in Western Europe by the Bell Beaker culture, despite a once mainstream view that the Bell Beaker culture did not have a major demic impact and largely had an impact on Western Europe through the dissemination of technology and trade goods. There is simply no other archaeological culture that can fit the ancient DNA facts as well.

Some Key Data Points

One substantial sample comes from Saint-Jean-et-Saint-Paul in inland Southern France ca. 3000 BCE, although this is arguably more in the Cardium Pottery Neolithic than the Atlantic megalithic cultural area.[29] This sample is very typical of first wave Neolithic populations in the LBK and at other Cardium Pottery sites with lots of Y-DNA G2a (20 men) and Y-DNA I2a (2 men) and no Y-DNA R1b. There was diversity of mtDNA that is not particularly heavy in mtDNA H. Specifically,
[Researchers obtained mtDNA haplotypes for] 29 of the 53 individuals tested. They were classified into 13 different haplotypes, which yielded a relatively high haplotype diversity . . . of 0.8966 ± 0.0354. . . . the 13 haplotypes previously found could be classified in 11 different haplogroups or subhaplogroups: H1, H3, HV0, V, K1a, T2b, U, U5, U5b1c, X2, and J1.
Another ancient DNA study with the same lead author looked at a first wave Neolithic sample from Spain ca. 5000 BCE, which found Y-DNA G2a and E1b1b1a1b and typical diverse early Neolithic mix of mtDNA halotypes (as opposed to an mtDNA H dominated sample), but again, no Y-DNA R1b [30]:
The impact of the Neolithic dispersal on the western European populations is subject to continuing debate. To trace and date genetic lineages potentially brought during this transition and so understand the origin of the gene pool of current populations, we studied DNA extracted from human remains excavated in a Spanish funeral cave dating from the beginning of the fifth millennium B.C. Thanks to a “multimarkers” approach based on the analysis of mitochondrial and nuclear DNA (autosomes and Y-chromosome), we obtained information on the early Neolithic funeral practices and on the biogeographical origin of the inhumed individuals. No close kinship was detected. Maternal haplogroups found are consistent with pre-Neolithic settlement, whereas the Y-chromosomal analyses permitted confirmation of the existence in Spain approximately 7,000 years ago of two haplogroups previously associated with the Neolithic transition: G2a and E1b1b1a1b. . . .

These results are highly consistent with those previously found in Neolithic individuals from French Late Neolithic individuals, indicating a surprising temporal genetic homogeneity in these groups. The high frequency of G2a in Neolithic samples in western Europe could suggest, furthermore, that the role of men during Neolithic dispersal could be greater than currently estimated.

Presently, few ancient data are available on the Neolithic period, and most of them consist of mitochondrial DNA data, which are only informative for the maternal origin. These have revealed a particularly high frequency of haplogroup N1a, a haplogroup quite rare currently in central European and in Atlantic coast Neolithic specimens, whereas this last was never found in southern European samples. These furthermore suggested a probable genetic continuity between ancient southern Neolithic specimens and current populations located in the same areas, whereas the ancient central European plains samples would share a greater affinity with the modern-day Near East and Anatolia. The findings deduced from the study of maternal genetic lineages seemed consistent with the archeological evidences of the existence of two distinct routes of neolithization: one along the central plains of Europe and another along the Mediterranean coasts.
A clearly relevant ancient data point comes from an Atlantic megalithic burial chamber in western France ca. 4200 BCE.[31]
Recent paleogenetic studies have confirmed that the spread of the Neolithic across Europe was neither genetically nor geographically uniform. To extend existing knowledge of the mitochondrial European Neolithic gene pool, we examined six samples of human skeletal material from a French megalithic long mound (c.4200 cal BC). We retrieved HVR-I sequences from three individuals and demonstrated that in the Neolithic period the mtDNA haplogroup N1a, previously only known in central Europe, was as widely distributed as western France. Alternative scenarios are discussed in seeking to explain this result, including Mesolithic ancestry, Neolithic demic diffusion, and long-distance matrimonial exchanges. In light of the limited Neolithic ancient DNA (aDNA) data currently available, we observe that all three scenarios appear equally consistent with paleogenetic and archaeological data. In consequence, we advocate caution in interpreting aDNA in the context of the Neolithic transition in Europe. Nevertheless, our results strengthen conclusions demonstrating genetic discontinuity between modern and ancient Europeans whether through migration, demographic or selection processes, or social practices.
I don't have access to the full text of the article and it does not have Y-DNA samples, but it is not dominated by mtDNA H, or apparently, by mtDNA U, to an extent that would be notable in the abstract of the paper.

A fourth sample provides ancient mtDNA from an early Neolithic Iberian population, which is also a Cardial Pottery culture.[32]
The Neolithic transition has been widely debated particularly regarding the extent to which this revolution implied a demographic expansion from the Near East. We attempted to shed some light on this process in northeastern Iberia by combining ancient DNA (aDNA) data from Early Neolithic settlers and published DNA data from Middle Neolithic and modern samples from the same region. We successfully extracted and amplified mitochondrial DNA from 13 human specimens, found at three archaeological sites dated back to the Cardial culture in the Early Neolithic (Can Sadurní and Chaves) and to the Late Early Neolithic (Sant Pau del Camp). We found that haplogroups with a low frequency in modern populations—N* and X1—are found at higher frequencies in our Early Neolithic population (∼31%). Genetic differentiation between Early and Middle Neolithic populations was significant (FST∼0.13, P < 10−5), suggesting that genetic drift played an important role at this time. To improve our understanding of the Neolithic demographic processes, we used a Bayesian coalescence-based simulation approach to identify the most likely of three demographic scenarios that might explain the genetic data. The three scenarios were chosen to reflect archaeological knowledge and previous genetic studies using similar inferential approaches. We found that models that ignore population structure, as previously used in aDNA studies, are unlikely to explain the data. Our results are compatible with a pioneer colonization of northeastern Iberia at the Early Neolithic characterized by the arrival of small genetically distinctive groups, showing cultural and genetic connections with the Near East.

The first wave Neolithic revolution Atlantic megalithic people of Western Europe, so far as the limited available ancient DNA evidence can tell us, bore a strong genetic resemblance to all of the other first farmers of Europe, about whom we have better ancient DNA data.

We know for a fact that across the board, although not always in precisely the same places at precisely the same times, the unprecedented population surge produced by the introduction of farming and herding to Western Europe was followed by an epic population crash that would put the Bubonic Plague to shame.

The modern European gene pool took its shape as the next major archaeological cultures, in the Copper and Bronze Ages, filled much of the vacuum created when the farming and herding economy collapsed the first time around, and expanded in a way that was effectively permanent.

In Eastern and Central Europe, this was the Indo-European Corded Ware culture.  But, in Western and Northern Europe, its technological equal, the Bell Beaker civilization and its immediate successors, held the Corded Ware culture at bay for a thousand years, until ultimately the climatic events of that precipitated the Bronze Age collapse tipped the balance in favor of Indo-European people - the linguistically Italic people in Italy (along with migrant Indo-European Greek colonies), the Celts in most of Western Europe and the British Isles, and the Germanic people in Northern Europe and Scandinavia.

Notwithstanding archaeological interpretations of the Bell Beaker culture as a thin superstrate of traders, metal workers and perhaps religious leaders.  The hard evidence from ancient and modern DNA, points strongly towards a major demic impact from these people in the 3rd millenium BCE, as they expanded their numbers at a record rate and evolved physically in a way that exploited their dairy farming prowess.

The subsequent Iron Age Celtic peoples conquered the region and had a moderate demic impact, while producing a language shift to their Vasconic substrate influenced Indo-European language in much of Europe.  The Romans and other waves of migrants that followed them had even less of a population genetic impact, although most of the people of the Celtic world ultimately came to speak another family of Indo-European languages under subsequent conquests, either Latin derived languages with a source in Rome, Italy, or Proto-Germanic derived languages that expanded and diversified out of origins Denmark.

Of course, suppose that we can conclude that the Bell Beaker people were the last and strongest force in shaping the modern Western European gene pool.

Suppose also that we can say with some comfort that the ultimate place of origin of Y-DNA haplotype R1b was in the highlands of West Asia.

The story of how the Bell Beaker people reached a secondary expansion focal point in Southern Portugal and went on to sweep Western Europe in the Copper Age and early Bronze Age remains an unsolved question although we have some tantalizing hints that have been suggested in this post, and previous posts at this blog.


[UPDATE: The references in this post have been significantly updated from the original post date through October 10, 2014, together with very minor changes in the body text.]

[1] Iosif Lazaridis, et al., "Ancient human genomes suggest three ancestral populations for present-day Europeans," (bioRxiv, Posted December 23, 2013) (examining autosomal DNA).
[2] Anna Szécsényi-Nagy et al., "Tracing the genetic origin of Europe's first farmers reveals insights into their social organization" (bioRxiv 2014).
[3] Doron M. Behar et al., "A 'Copernican' Reassessment of the Human Mitochondrial DNA Tree from its Root," (The American Journal of Human Genetics, Volume 90 (2012), supplement) (arguing for a Neolithic dispersal, possibly from the Near East).
[4] Antonio Torroni et al., "mtDNA Analysis Reveals a Major Late Paleolithic Population Expansion from Southwestern to Northeastern Europe," (American Journal of Human Genetics, vol. 62 (1998)) at pp. 1137–1152 (arguing for a Mesolithic dispersal from a Franco-Cantabrian refugium).
[5] Wolfgang Haak et al,, "Ancient DNA from the First European Farmers in 7500-Year-Old Neolithic Sites" (Science, Vol 310, Issue 5750, 1016-1018 , 11 November 2005) (the study looked at 24 mtDNA samples from members of the LBK culture ca. 5500 BCE from multiple locations)
[6] Sampietro ML, et al., "Palaeogenetic evidence supports a dual model of Neolithic spreading into Europe." (Proc Biol Sci. 2007 Jun 26; Epub ahead of print) (the study looked at mtDNA from "11 Neolithic remains from Granollers (Catalonia, northeast Spain) dated to" 3500 years BCE).
[7] Timpson et al, "Reconstructing regional population fluctuations in the European Neolithic using radiocarbon dates: a new case-study using an improved method" (Journal of Archaeological Science 2014).
[8] Lee EJ, et al. "Emerging genetic patterns of the european neolithic: Perspectives from a late neolithic bell beaker burial site in Germany" (American Journal of Physical Anthropology 2012).
[9] Wolfgang Haak et al. "Ancient DNA, Strontium isotopes, and osteological analyses shed light on social and kinship organization of the Later Stone Age" (PNAS 2008).
[10] I. Lazaridis, et al., "Capture of 390,000 SNPS in dozens of ancient central Europeans reveals a population turnover in Europe thousands of years after the advent of farming.", American Society of Human Genetics (ASHG) 2014 Conference Abstracts (to be delivered October 18-22, 2014) (via Dienekes Anthropology Blog).
[11] Jeffery R. Hughey, et al., "A European population in Minoan Bronze Age Crete", (Nature Communications 2013) (sample size N=37).
[12] Laisel Martinez, et al., "Paleolithic Y-haplogroup heritage predominates in a Cretan highland plateau" (European Journal of Human Genetics advance online publication 31 January 2007).
[13] King RJ, et al., "Differential Y-chromosome Anatolian influences on the Greek and Cretan Neolithic" (2008 Ann Hum Genet 72:205–214).
[14] Eva Fernandez, et al., "Ancient DNA Analysis of 8000 B.C. Near Eastern Farmers Supports an Early Neolithic Pioneer Maritime Colonization of Mainland Europe through Cyprus and the Aegean Islands" (PLOS Genetics June 5, 2014)
[15] Viola Grugni et al., "Ancient Migratory Events in the Middle East: New Clues from the Y-Chromosome Variation of Modern Iranians" (PLoS ONE 2012).
[16] Bayazit Yunusbayev et al., "The Caucasus as an asymmetric semipermeable barrier to ancient human migrations" (Mol Biol Evol 2011)
[17] Kristian J Herrera, et al., "Neolithic patrilineal signals indicate that the Armenian plateau was repopulated by agriculturalists" (European Journal of Human Genetics 16 November 2011)
[18] Ömer Gokcumen et al., "Biological Ancestries, Kinship Connections, and Projected Identities in Four Central Anatolian Settlements: Insights from Culturally Contextualized Genetic Anthropology" (2011 American Anthropologist Volume 113, Issue 1, pages 116–131) (about 10% of Y-DNA is R1b in this Central Anatolian region, but one must observe that many ethnically Greek and Armenian people who had Y-DNA R1b and once lived in Anatolia were exiled or exterminated in recent history).
[19] Underhill, et al., "The phylogenetic and geographic structure of Y-chromosome haplogroup R1a" (Eur J Hum Genet. 2014 Mar 26).
[20] I.M. Diakonoff, "The early Trans-Caucasian culture" (1984) (suggesting a demise of the culture ca. 2000 BCE).
[21] Edens, Christoper, "Transcaucasia at the End of the Early Bronze Age" (Bulletin of the American Schools of Oriental Research Aug–Nov 1995) (suggesting a demise of the culture ca. 2700-2600 BCE).
[22] Mariya Ivanova, "Kaukasus und Orient: Die Entsthung des "Maikop-Phanomens" im 4. Jahrausend .Chr.", 87(1) Prahistorische Zeitschrift 1-28 (2013) (in German) (abstract translated at Dienekes Anthropology Blog).
[23] Alexei Kassian, "Lexical Matches between Sumerian and Hurro-Urartian: Possible Historical Scenarios" (Cuniform Digital Library Journal Preprint October 3, 2014).
[24] Arnaud Fournet, "The Kassite Language In a Comparative Perspective with Hurrian and Urartean" (The Macro-Comparative Journal 2010).
[25] Konstatine Pitskhelauri, "Uruk Migrants in the Caucuasus", (6(2) Bulletin of the Georgian National Academy of Sciences 2012)
[26] Vankan P., "Prevalence gradients of Friedreich's ataxia and R1b haplotype in Europe co-localize, suggesting a common Palaeolithic origin in the Franco-Cantabrian ice age refuge" (J Neurochem. August 2013).
[27] D'Amore G, et al., "Craniofacial morphometric variation and the biological history of the peopling of Sardinia." (Homo. 2010 Oct 25 Epub ahead of print) (skull shape in Sardinia shows continuity from the Neolithic era through the Bronze Age and into the present and are distinct from Etruscan skulls and have skulls more distinct from modern Italian skulls than from early Neolithic Italian skulls).
[28] Silvia Ghirotto et al., "Inferring Genealogical Processes from Patterns of Bronze-Age and Modern DNA variation in Sardinia" (Molecular Biology and Evolution 2009) (Bronze Age mtDNA in Sardinia N=23 shows strong continuity with modern mtDNA variation in Sardinia).
[29] Marie Lucan, et al, "Ancient DNA reveals male diffusion through the Neolithic Mediterranean route" (PNAS open access June 14, 2011).
[30] Marie Lucan, et al., "Ancient DNA suggests the leading role played by men in the Neolithic dissemination" (PNAS open access November 8, 2011).
[31] Marie-France Deguilloux, et al., "News from the west: Ancient DNA from a French megalithic burial chamber" (American Journal of Physical Anthropology August 17, 2010).
[32] C. Gamba, "Ancient DNA from an Early Neolithic Iberian population supports a pioneer colonization by first farmers" (Molecular Ecology January 2012).