Thursday, August 17, 2017

Data Points About The Mostly Iberian Y-DNA Clade R1b-DF27


A new paper explores the predominantly Iberian branch of Y-DNA haplogroup R1b which is timely because the narrative that explains the population genetics of Iberia is much less clear than most other places in Europe.


The most common Y-DNA clade in Western Europe is R1b-M269. As Bernard's Blog explains (note that all translations are Google translated from the original French with my editorial improvements of those translations):
The most important branches of M269 are U106 common in the Netherlands and Northwestern Germany, and P312 common in Western Europe. The latter is divided into three main branches: U152 common in Switzerland and Northern Italy, L21 common in the British Isles and DF27 frequent in the Iberian Peninsula.
Y-DNA R1b-DF27 predominant in Iberia and especially in Basques and parts of Eastern Spain that were Vasconic linguistically in historically attested times. 

This Y-DNA R1b clade is a sister clade to the R1b haplogroups found in the British Isles and in Switzerland and Northern Italy. But, it is a more distant relative of the R1b clades around in the Netherlands and Northwest Germany (which is close to the area where the Germanic languages emerged, probably much later based upon linguistic evidence).

The new blog post focuses on a paper analyzing Y-DNA R1b-DF27 which is the most common in Iberia (especially Basque territory and Catalonia), and spills over into France as illustrated in the geographic distributions below:


DF27 is found at a frequency ranging from 30% to 50% in the Iberian Peninsula except in the Basque Country where Frequency reached 74%. In France, the frequency varies from 6% to 20% with an average of 11%. Elsewhere the frequency is 15% in Great Britain but almost nil in Ireland and 8% in Tuscany.
The subclade just downstream of DF27 is Z195. The frequency of the latter varies from 29% to 41% with two main peaks in the Basque Country and in Eastern Spain. Then Z195 divides into two main branches: L176 and Z220. L176 has a peak frequency in Eastern Spain while Z220 has a peak frequency in the Basque Country.
The inferred ages of these clades coincides well with an arrival fairly early in the Bell Beaker era, followed by local differentiation.

Within each population, DF27 is older in Aragon (4530 years) than in the Basque Country (3930 years). Z195 is older in Catalonia (4580 years) In the Basque Country (3260 years). Conversely, Z220 is older in Central North Spain (3720 years). Thus, the greater diversity in eastern Spain and the older age in this same region, point towards an origin of the haplogroup R1b-DF27 in eastern Spain.
Models of Bayesian analysis show that DF27 extended in the Iberian Peninsula mainly between 3500 and 3000 years, i.e. in the Middle Bronze Age. These results are to be compared with those of ancient DNA in Portugal which show the dominance of haplogroup R1b in the Middle Bronze Age. This points to an origin of the haplogroup R1b-DF27 in eastern Spain. 
Analysis

Our access to ancient DNA is limited, but the ancient Iberian Bell Beaker DNA that we do have shows quite modest levels of autosomal steppe ancestry, but basically total replacement of Y-DNA R1b, which would be consistent with a male dominated migration event that was diluted in autosomal impact by multiple generations of marriages to non-steppe women with early European farmer and Western hunter-gather ancestry.

If Y-DNA R1b-DF27 mere were the source of the Bell Beaker phenomena, one would expect an age for the clade of about 4900 years and a point of origin based on clade ages and maximum diversity in Southern Portugal. But, that isn't what we see. Indeed, many important sub-clades of Y-DNA R1b-DF27 are entirely absent from Portugal and the clades we do see are heavily concentrated within Iberia in historically attested Vasconic areas, casting doubt on the hypothesis of a broader Vasconic linguistic area, particularly within Iberia.

Origins for R1b-DF27 in Eastern Spain ca. 2600 BCE to 2500 BCE suggest a maritime or southern European coastal route of these R1b men into Spain. The location of the Northern Italian sister clade of DF27 also supports a maritime or coastal route. This is several hundred years after the Bell Beaker phenomena begins in Southern Portugal ca. 2900 BCE. Presumably, these men adopt the Bell Beaker culture when it expands to their territory, rather than playing a part in its formation.

Combined Dark Dark Matter Detection Experiment Exclusions

A new pre-print combines the exclusion areas of the leading direct dark matter detection experiments which leads to a stronger combined exclusion (it does not integrate particle collider exclusions, however).

The bottom line is that the combined exclusion clearly rules out any weakly interacting massive particle (WIMP) with a weak interaction coupling even close to that of a neutrino, in the WIMP mass range from about 10 GeV to 1000 GeV. The exclusion is strongest in the WIMP mass vicinity of 20 GeV to 30 GeV, where it is at least twenty times as weak as at the edge of this exclusion range.

The relative strength of the exclusions doesn't really have much of anything to do with the data actually gathered which has come up with no reliably observed events ever (a handful of false positives have been ruled out by non-replication of those findings by other experiments sensitive to the purported mass and cross-section of interaction of the false positive results). They are simply a product of the sensitivity of the experimental setup to various kinds of hypothetical WIMPS.

The sensitivity of these experiments deteriorates greatly for WIMP masses below 10 GeV. And, a major theoretical bound on the methodology used by these experiments, the lower "neutrino bound" when background static from interactions cased by neutrinos makes it difficult or impossible to distinguish dark matter interactions from neutrino interactions is only about two orders of magnitude away.

At the higher mass scale, there aren't any real theoretical barriers to detecting heavier WIMPS, the the sensitivity of the experiments declines much more gradually in ruling out heavier WIMP candidates, but the experiments are simply not tuned to look for heavier candidates.

This result directly challenges a huge part of the supersymmetry parameter space, because SUSY theories, generically, give rise to dark matter candidates in the 10 GeV to 1000 GeV mass range that should have cross-sections of interaction as a result of the weak force strong enough to be detected by these experiments.

Of course, this limits of the WIMP mass range that is excluded doesn't necessarily mean that spending a lot to probe potential WIMP masses of more than 1000 GeV or a bit less than 10 GeV make much sense. 

If dark matter is truly collisionless (i.e. lacks any electromagnetic, strong force or weak force interactions), no direct dark matter detection experiment will ever find it. 

And, multiple lines of independent astronomy based data strongly disfavors Cold Dark Matter theories generally, which certainly includes all WIMP candidates in the 1 MeV to 10 GeV and in the greater than 1000 GeV range.

In other dark matters news, observations of dwarf galaxies that appear to have a dark matter to ordinary matter mass ratio on the order of 1000-1 by the HESS telescopes have not detected any signatures of dark matter particle annihilation, which imposes significant constraints on the dark matter particle parameter space. The exclusion is particularly strong in the 400 GeV to 1000 GeV WIMP mass range.

Wednesday, August 9, 2017

Modern Humans Reached Indonesia Shortly After The Toba Erruption

The Toba mega volcano eruption took place about 75,000 to 74,000 years ago.
Toba Lake in northern Sumatra is the world's largest active volcanic caldera. The volcanic eruption that resulted in Lake Toba (100 x 30 km) 74,000 years ago, is known to have been by far the biggest eruption of the last 2 million years. This mega-bang caused a prolonged world-wide nuclear winter and released ash in a huge plume that spread to the north-west and covered India, Pakistan, and the Gulf region in a blanket 1–5 metres (3–15 feet) deep. Toba ash is also found in the Greenland ice-record and submarine cores in the Indian Ocean, allowing a precise date marker. . . . the Toba eruption is the most accurately dated, dramatic, and unambiguous event before the last ice age.
Very shortly after that eruption, we find the oldest reliably dated modern human presence in what is now called Sumata, Indonesia, which is in Island Southeast Asia. We also know that modern humans were present in India prior to the Toba eruption based upon lithic tools of types (of the same type across the Toba ash barrier) associated only with modern humans that have been found both above and below Toba ash there.

It seems likely that the Toba eruption opened up a biogeographic barrier that had confined modern humans to India before then, possibly by thinning out dense forests and shrinking existing hominin populations in the region. 

I'd love to see ancient DNA from the teeth sampled here to see if they had Denisovan admixture, to look at the timing of their Neanderthal admixture, and to see how much of the genetic diversity present in these samples is still found in Southeast Asian populations. It would also clarify the timing of different waves of migration associated with particular uniparental genetic markers.
Genetic evidence for anatomically modern humans (AMH) out of Africa before 75 thousand years ago (ka) and in island southeast Asia (ISEA) before 60 ka (93–61 ka) predates accepted archaeological records of occupation in the region. Claims that AMH arrived in ISEA before 60 ka have been supported only by equivocal or non-skeletal evidence AMH evidence from this period is rare and lacks robust chronologies owing to a lack of direct dating applications, poor preservation and/or excavation strategies and questionable taxonomic identifications. 
Lida Ajer is a Sumatran Pleistocene cave with a rich rainforest fauna associated with fossil human teeth. The importance of the site is unclear owing to unsupported taxonomic identification of these fossils and uncertainties regarding the age of the deposit, therefore it is rarely considered in models of human dispersal. 
Here we reinvestigate Lida Ajer to identify the teeth confidently and establish a robust chronology using an integrated dating approach. Using enamel–dentine junction morphology, enamel thickness and comparative morphology, we show that the teeth are unequivocally AMH. Luminescence and uranium-series techniques applied to bone-bearing sediments and speleothems, and coupled uranium-series and electron spin resonance dating of mammalian teeth, place modern humans in Sumatra between 73 and 63 ka. This age is consistent with biostratigraphic estimations, palaeoclimate and sea-level reconstructions, and genetic evidence for a pre-60 ka arrival of AMH into ISEA. Lida Ajer represents, to our knowledge, the earliest evidence of rainforest occupation by AMH, and underscores the importance of reassessing the timing and environmental context of the dispersal of modern humans out of Africa.
K. E. Westaway, et al., "An early modern human presence in Sumatra 73,000–63,000 years ago" Nature(August 9, 2017) (Pay per view) doi:10.1038/nature23452

A newspaper account of the paper's findings with photographs can be found here.