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, 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.

Relic 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 Corsia, 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, but 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 of 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, showing signs of linguistic connection to and wife taking from Cushitic people, probably in Southern Sudan.  But, this was not shares 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 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 which 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), and 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 domesticate 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.

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 only 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 H were common, while Y-DNA R1, J2 and G that are predominant in early European 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 largely in Dravidian areas of Southeastern India that did not adopt agriculture until around 2500 BCE using mostly African Sahel crops, probably arrived in India at that time, and was 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 (and area that in the Copper Age had thriving maritime trade with the Indus River Valley).

After all, 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.

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 G and T, but there is very little Y-DNA R1 that is not traceable to the historic era, and Y-DNA 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, 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 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, it was not largely a story of pure 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 that 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.

Sunday, December 14, 2014

Quick Anthropology Hits

Africa

* 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.

Europe

* 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.