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.

Tuesday, August 8, 2017

Muons Are Weird. Is An Electron-Phobic Scalar Boson To Blame?

In the Standard Model, a muon is simply an electron with a bigger mass. 

But, measurements of the radius of muonic hydrogen and the muon magnetic dipole moment (muon g-2), show a fairly significant discrepancy between theory an experiment in that respect, at the five sigma and three sigma levels, respectively. There are also indications from B meson decays that the lepton universality is violated by the charged leptons (i.e. the muons and electrons do not behave identically apart from the differences predicted as a result of their respective masses).

A new PhD thesis by Yu-Sheng Liu at the University of Washington explores what kind of new physics could give rise to this discrepancy. The thesis concludes that a scalar boson whose couplings to the charged leptons differ by the ratio of the muon mass to the electron mass (mu/me)^n for some n>1 could resolve the subtle discrepancy between theory and experiment. In this theory, the new scalar boson couples more strongly to muons than to electrons. 

The  thesis then looks at the experimental bounds on the relevant coupling constants of this minimally flavor violating scalar boson. A vector boson or much of the rest of the parameter space (e.g. n<1) is ruled out.

The paper does not suggest how such an electron-phobic scalar boson would fit into any larger theoretical model, for example, at high energies.

While there are many possible explanations for the observed discrepancies, the most plausible of which involve experimental measurement issues, understated error bars and flawed theoretical calculations using Standard Model physics, this humble but thorough study presents one of the most plausible beyond the Standard Model theories to explain these phenomena that I have seen to date.

Ancient People In Forests and Jungles

While some of the dates are doubtful or probably represent archaic hominins, rather than modern humans, there is no doubt that people have lined in forests and jungles for a very long time.
In the last ten years, the archaeologically-acknowledged start date of human inhabitation of tropical forests has quadrupled in age. There is now clear evidence for the use of tropical forests by our species in Borneo and Melanesia by c. 45 ka; in South Asia by c. 36 ka; and in South America by c. 13 ka. There are suggestions of earlier rainforest occupation c. 125 ka in Java, c. 60 ka in the Philippines, c. 100 ka in China, and in Africa perhaps from the first appearance of Homo sapiens c. 200 ka, though further research is required to verify these cases.

Early modern humans adapted to diverse tropical forest formations, ranging from the sub-zero temperatures of montane forests to dense, humid, evergreen rainforests, undertaking sophisticated forest mammal hunting and plant processing. Moreover, people did not just adapt passively to these environments, but from the onset modified them in fundamental ways, with outcomes that have affected the natural histories of these forests to the present day.

Monday, August 7, 2017

The Neanderthal-Denisovan Branch Of Hominins

A new paper on archaic hominins opens with this abstract and an introductory paragraph as follows:
Extensive DNA sequence data have made it possible to reconstruct human evolutionary history in unprecedented detail. We introduce a method to study the past several hundred thousand years. Our results show that (i) the Neanderthal–Denisovan lineage declined to a small size just after separating from the modern lineage, (ii) Neanderthals and Denisovans separated soon thereafter, and (iii) the subsequent Neanderthal population was large and deeply subdivided. They also (iv) support previous estimates of gene flow from Neanderthals into modern Eurasians. These results suggest an archaic human diaspora early in the Middle Pleistocene. 
Around 600 kya, Europe was invaded by large-brained hominins using Acheulean stone tools. They were probably African immigrants, because similar fossils and tools occur earlier in Africa. They have been called archaic Homo sapiens, Homo heidelbergensis, and early Neanderthals, yet they remain mysterious. They may have been ancestors of Neanderthals and modern humans, or ancestors of Neanderthals only, or an evolutionary dead end. According to this last hypothesis, they were replaced later in the Middle Pleistocene by a wave of African immigrants that separated Neanderthals from modern humans and introduced the Levallois stone tool tradition to Europe. To address this controversy, we introduce a statistical method and use it to study genetic data of Africans, Eurasians, Neanderthals, and Denisovans.
Alan R. Rogers, Ryan J. Bohlender and Chad D. Huff. "Early history of Neanderthals and Denisovans" (PNAS August, 2017) doi: 10.1073/pnas.1706426114

The body text explores the mostly likely date of the split of the ancestors of modern humans from Neanderthals, and concludes that the evolutionary dead end hypothesis is not correct:
Our own date estimates inherit the uncertainty of the molecular clock. Using the YRI.CEU data, our point estimate of the Neanderthal–Denisovan separation time is 744 kya. Many authors prefer a higher mutation rate of 5×10^−10 per nucleotide site per year. Under this clock, our estimate becomes 616 kya.
Further along it notes:
[O]ur results also disagree with previous estimates of the Neanderthal–Denisovan separation time. On the other hand, Meyer et al. show that 430 ky-old fossils from Sima de los Huesos, Spain are more closely related to Neanderthals than to Denisovans. This implies an early separation of the two archaic lineages. Our own estimate—25,660 generations, or 744 ky—is earlier still. It is consistent with the results of Meyer et al.  but not with those of Prüfer et al., as discussed above. The cause of this discrepancy is unclear. Prüfer et al. use the pairwise sequentially Markovian coalescent (PSMC) method, which may give biased estimates of separation times in subdivided populations. 
Our results shed light on the large-brained hominins who appear in Europe early in the Middle Pleistocene. Various authors have suggested that these were African immigrants. This story is consistent with genetic estimates of the separation time of archaics and moderns. Our own results imply that, by the time these hominins show up in European archaeological sites, they had already separated from Denisovans. This agrees with Meyer et al., who show that the hominins at Sima de los Huesos were genetically more similar to Neanderthals than to Denisovans. It also agrees with Hublin, who argues that Neanderthal features emerged gradually in Europe, over an interval that began 500–600 kya.
How small was the population ancestral to Neanderthals and Denisovans before the regional split of the two species?
During the interval between the two separation events, the ancestral archaic population was apparently very small. Our point estimates of 2N(ND) range from about 100 to about 1,000, with narrow confidence intervals. Following the Neanderthal–Denisovan separation, our results imply a relatively large Neanderthal population, with 2N in the tens of thousands.
Analysis

Thus, it is increasingly looking like there were at least three waves of hominins Out of Africa and into Eurasia, and there could easily have been as many as six (including two modern human waves, two Homo erectus waves, and a wave associated with Homo floresiensis). It isn't inconceivable that new discoveries could support additional waves of hominin Out of Africa migration, although there is really no evidence to support that at this time.

Also, our time resolution degrades as we get into the more remote past. For example, it would be almost impossible to determine if the Homo erectus wave was really a single migration, or was actual several migrations spaced 25,000 to 50,000 years apart from each other. What looks like it might have been two waves of modern humans leaving Africa from our vantage point, would look like a single wave of migration if we were looking at the evidence from a vantage point a million years in the future.

Wave One: Homo Erectus

The first hominin Out of Africa wave occurred about 1,900,000 years ago with Homo erectus. Some of the Homo erectus who stayed in Africa probably evolved into an archaic hominin species which is the common ancestor of modern humans, Neanderthals and Denisovans. (Homo ergaster is now mostly seen as a primitive and transitional species directly ancestral to and arguably part of the species Homo erectus, which in turn probably evolved from Homo habilis.)
Early African Homo erectus fossils (sometimes called Homo ergaster) are the oldest known early humans to have possessed modern human-like body proportions with relatively elongated legs and shorter arms compared to the size of the torso. These features are considered adaptations to a life lived on the ground, indicating the loss of earlier tree-climbing adaptations, with the ability to walk and possibly run long distances.
The spread of Acheulian stone tool technology, which was not possessed by the first Homo erectus to leave Africa, suggests that around 1,500,000 to 1,400,000 years ago, there was a secondary wave either of a second wave of Out of Africa migrating Homo erectus, or of cultural diffusion between Homo erectus of stone tool technology from Africa.
Current thinking is that Acheulian technology originated in East Africa (possibly West Turkana, Kenya) at least 1.76 million years ago (Ma), that it became distributed somewhat widely across Africa (e.g., Vaal River Valley and Gona) at ∼1.6 Ma, and then spread to the Levant at ∼1.4 Ma, South Asia at 1.5–1.1 Ma, and Europe at 1.0–0.9 Ma. The 0.8–0.9 Ma Acheulian stone stools from South and central China suggest that Acheulian technology arose in China at least during the terminal Early Pleistocene. However, there are only a few sites with in situ Acheulian artefacts from North China with ages ranging from the late Mid-Pleistocene to the Late Pleistocene. [Ed. Later the paper dates the oldest sites in North China to 0.9 Ma.]
From this paper (with citations to the literature from 1993 through 2014 omitted).

Wave Two: Proto-Neanderthal-Denisovan

The second hominin Out of Africa wave occurred around 745,000 to 600,0000 years ago that gave rise to a common Neanderthal-Denisovan lineage (which was probably synonymous with Homo heidelbergensis) that in turn split into two regional branches. The lineage ancestral to modern humans (who became a distinct species about 300,000 to 200,000 years ago) was not distinct from the lineage ancestral to Neanderthals and Denisovans at that point.

In this scenario, the Levallois stone tool tradition in Europe was a local Neanderthal development in the Middle Pleistocene, that was apparently not shared with or paralleled by the Denisovan hominins from whom they had separated hundreds of thousands of years before, perhaps because their smaller effective population impeded their ability to improve upon the Acheulian stone tools they used when they left Africa and then split from the Neanderthals.

What About The Denisovan?

The dog that isn't barking in this hypothesis is the Denisovan lineage which appears to have migrated to the east, relative to Neanderthals.

We have extensive fossil and archaeological tool evidence of the Neanderthal branch of the Homo heidelbergensis tree, and pretty good evidence of the Homo sapiens branch. But, we have only the slightest evidence of what the Denisovan lineage, which apparently did not see the population expansion that the proto-Neanderthals did, was doing for 400,000 or more years between their separation from Neanderthals and their admixture with modern humans ancestral to Papuan and Australian modern humans.

What was the Denisovan range?  How was the Denisovan range impacted by the pre-existing Homo erectus population? Did the Denisovan people replace Homo erectus in fairly short order, or did they co-exist with them?

Are the oldest hominin remains in China that aren't clearly Homo erectus really Denisovans (perhaps highly evolved from the time they left Africa)? Or, are they hybrids of modern humans and Denisovans?

Or, are they some other branch of the hominin tree entirely (e.g. highly evolved Homo erectus or a previously entirely unknown archaic hominin species from Africa), with or without modern human admixture?

This final option puts pressure on the principle of parsimony, since it would require either another wave of Out of Africa hominin migration with no obvious African candidate, or in situ evolution not demonstrated with transitional fossils anywhere in a 1.5 million year plus time span. But, parsimony has not been a terribly reliable principle for investigators looking at hominin evolution in recent years.

What about Homo floresiensis?

In particular, there are fairly strong indications that Homo floresiensis may actually have been either a different more primitive hominin species than Homo erectus, perhaps a close relation of Homo habilis who evolved ca. 2,400,000 years ago (about 400,000 years before Homo erectus, but overlapping with it for about 600,000 years in Africa) and is the oldest definitively identified member of the genus Homo.

Homo habilis was more adapted for a life in the trees (as opposed to walking longer distances on the ground) than Homo erectus, used more primitive stone tools than Homo erectus, and while also an omnivorous meat eater had a diet that was more plant heavy and lighter on meat than Homo erectus who ate "some tougher foods like leaves, woody plants, and some animal tissues, but that they did not routinely consume or specialize in eating hard foods like brittle nuts or seeds, dried meat, or very hard tubers." Homo erectus used fire (although it isn't clear just how much mastery they had over it) while Homo habilis did not - which would have encouraged Homo habilis to live in places not easily razed by intentionally set forest and brush fires (a key tool used by Australian Aborigines to defeat impressive Australian megafauna).

Homo habilis averaged 3 foot 4 inches to 4 foot 5 inches and averaged about 70 pounds, consistent with Homo floresiensis which averaged about 3 foot 6 inches. In contrast, Homo erectus had body proportions similar to modern humans an averaged 4 foot 9 inches to 6 foot 1 inch, and averaged about 88-150 pounds.

So, it is possible to image that Homo erectus and Homo habilis could have co-existed in different ecological niches in Asia, with Homo habilis favoring dense Asian jungles, while Homo erectus favored lightly wooded area and other more open spaces similar to the African savannah which may have been favored by their ancestors.

Homo floresiensis or its ancestors, could have been a fellow traveler with Homo erectus or Homo heidelbergensis, or may have arrived in a separate Out of Africa migration of its own.

Oldowan stone tools, normally associated with Homo habilis in Africa, are found in Asia from very ancient times until about 200,000 to 300,000 years ago.

The earliest hard evidence of Homo floresiensis is only about 190,000 years old on the island of Flores (implying that "Hobbits" still left Africa well before the earliest modern human departure from Africa in any scenario), but this could simply be due to a lack of well preserved evidence of them in mainland Asia and island Southeast Asia to the west of the Wallace line.

There is a wide time frame in which the small population of Homo habilis-like hominins necessary to give rise to the relict population that survived until after modern humans evolved on Flores, could have left Africa (really any time from 2,400,000 years ago to 200,000 years ago).

But, a migration in the roughly 500,000 year long pre-Homo erectus migration time period would seem to make the most sense. The youngest Homo habilis remains found in Africa date to 1,400,000 years ago reducing the likelihood of a migration of a relict population long after that date, but after Homo erectus left Africa, Homo habilis would face tough competition in Eurasia.

Still, once out of Africa and past the Middle East, there would have been some places in Asia where a small Homo habilis population could have survived competition with Homo erectus. Their best strategy may have been to stay out of the way of the larger members of genus Homo, such as in jungles better suited to smaller hominins.

Most importantly, Homo floresiensis could not have been the source of Denisovan ancestry in modern humans in Papua New Guinea and Australia, even though the only location where their remains are observed is perfectly located to fit the distribution of Denisovan ancestry in modern humans.

Some Wild Speculations About A Hobbit/Denisovan/Homo Erectus Pre-History Narrative

Indeed, speculatively, the appearance of Homo floresiensis on the island of Flores around 190,000 years ago could have been the culmination of their desperate flight from the Denisovans, leading the Hobbits to take a chance on driftwood rafts across the strait to Flores, a trip that the predatory Denisovans weren't willing to risk. Perhaps Denisovans, as they arrived in Southeast Asia were sufficiently smart and versatile to pose a genocidal threat to the Hobbits, even in their jungle-like environments which had protected them in the past because these environments were less well suited to Homo erectus, who also had less of an edge in intelligence over the Hobbits and were more rigid and ecologically inflexible than the Denisovans.

This scenario also puts Denisovans in the right place, at the right time to explain the geographic pattern of their introgression into modern humans, while making their arrival recent enough and brief enough (assuming that all of the Denisovans were in turn dispatched or assimilated by modern humans) that we would not expect them to leave much of an archaeological trace in Southeast Asia.

This scenario also coincides fairly well with a time period in which there are relatively few traces of Homo erectus in Asia. About 300,000 to 200,000 years ago, stone tools made with the Oldowan technology, previously associated with Asian Homo Erectus and with African Homo habilis disappear. If Denisovans had a lighter archaeological footprint than Homo erectus, one would expect a gap in the hominin archaeological record during a period in which Denisovans partially or entirely replaced Asia's Homo erectus population. The last Homo erectus remains date to 143,000 years ago in Indonesia which would have been the last frontier in a wave of Denisovan expansion if this narrative bears any resemblance to reality.

The appearance of Acheulian tools in China around 800,000 to 900,000 years ago, could coincide with the arrival of the first Denisovans in Asia, who may have co-existed with Homo erectus (and perhaps Homo habilis as well) for about 500,000 years or more in Asia.

The lack of Acheulian tools in Asian Homo erectus (at least until the Denisovans arrive in Asia) unlike Homo erectus in Africa, Europe and South Asia who made this innovation much earlier (and before the migration of Homo heidelbergensis out of Africa) may have also made it possible for Homo habilis to avoid the extinction at the hands of Homo erectus that it experienced in Africa where the adoption of Acheulian tools by Homo erectus/ergaster and the demise of Homo habilis come fairly close in time.

A Denisovan surge, after hundreds of thousands of years to the north of Homo erectus territory and perhaps co-existing with Homo erectus in China, might reflect some paradigm shifting cultural innovation that the Denisovan's developed around that time in lieu of the Levallois stone tool tradition developed around that time by their Neanderthal cousins in Europe. This unspecified cultural innovation may have given them an edge in hunting and warfare compared to their previous, rather marginal selective fitness in Eurasia that finally made them clearly superior to both Homo erectus and Homo habilis who might have been found, until then, in different ecozone of Asia.

Perhaps this Denisovan breakthrough that finally allowed them to become dominant was an innovation with a light archaeological footprint such as something comparable to the development of bamboo weapons, or frog poison blow darts, or an advance in language abilities, as opposed to more advanced stone tools than they had from the outset. Or perhaps, the break through was a matter not of technology, but of a major climate event that the more intelligent Denisovans managed to survive better than the duller and more rigid Homo erectus and Homo habilis.

Perhaps, by the time modern humans arrived in Asia, the Denisovan has brought about the extinction of Homo erectus and Homo habilis in all but a few small relict communities in Asia, a favor that modern humans returned by causing the extinction and/or assimilation of all of the remaining Denisovans around 75,000 to 65,000 years ago, or perhaps earlier, with an initial boost created by the ecological disruption arising from the Toba super volcano explosion.

Wave Three: Modern Humans

A third hominin Out of Africa wave brought Homo sapiens, with a first Homo sapien Out of Africa wave about 125,000 to 100,000 years ago and possibly with a second wave of Homo sapiens to leave Africa about 75,000 to 60,000 years ago. It isn't clear if the second Homo sapiens Out of Africa wave is derived from the first Homo sapiens Out of Africa wave, or if the second Homo sapiens Out of Africa wave was separate from the first, with the first wave being largely a dead end leaving only some Middle Eastern relics and some admixture of ancestors of the Altai Neanderthals. We have very little evidence to guide us one way or the other.

Loose ends in Africa

It is fairly likely that other archaic hominin species with admixed with modern humans within Africa who can only be identified as "ghost populations" in African whole genomes right now may also have arisen from this Homo heidelbergensis lineage as well with one study noting that: "On the basis of an excess of shared derived alleles between San, Neanderthal, and Denisova we suggest that a third archaic population related more closely to Neanderthal and Denisova than to modern humans introgressed into the San genomes studied here." The admixture with the San probably took place in the last 100,000 years.

There was also probably another archaic admixture, possibly with a different "ghost species" in Africa, that impacted the African Pygmy genome.

An unknown archaic species that broke off from the lineage that includes Homo heidelbergensis about 3,450,000 years ago (quite possibly, given the timing, the pre-Homo species affectionately known as "Lucy" a.k.a. Australopithecus afarensis or Australopithecus africanusfor whom 3.45mya is a bit of a stretch, but which persists much later than Lucy) may have introgressed into a quite basal version of Homo heidelbergensis.

Homo naledi in Southern Africa is a recently discovered diminutive species of archaic hominins that still existed when modern human evolved (those found are from 300,000 to 200,000 years ago), although their remains suggest that they are part of a fairly archaic and basal branch of the human evolutionary tree, with estimates based upon how archaic its features were in the range of 2,500,000 to 912,000 years ago.

Homo rudolfensis known from only one decent set of remains from about 1,850,000 years ago that was discovered in Kenya in 1986 seems similar to Homo habilis but with a larger brain case. It isn't clear exactly where this specimen belongs in the evolutionary tree.

Other Archaic Hominin Stories

In other archaic hominin news, John Hawks muses over why stable hybrid zones apparently didn't emerge between Neanderthals, Denisovans and modern humans respectively.

As the above discussions suggest, however, even if stable hybrid zones didn't emerge in Eurasia, they probably did exist for some extended periods of time in parts of Africa, where hominins originated and hominin populations were larger. Some of the populations in Eurasia may have been too greatly diverged from each other, and too small in effective population size themselves, to give rise to reasonably sized stable hybrid populations.

Ancient Mesopotamian mtDNA

Once again, ancient DNA evidence shows that the paternal Y-DNA makeup of a population is more prone to shifting than its maternal mtDNA population. It is particularly notable that there is not a strongly discernible shift towards Caucasian/Iranian mtDNA as this shift is visible in the Y-DNA and autosomal DNA of the region in the same time period, as shown by other recent ancient DNA work.

This suggests in this particular case that greater Syrian population genetic change in the Holocene has been driven by male dominated introgression among elites, rather than by gender balanced folk migration. This sample does not, however, include population genetic shifts attributable to the rise of the Islamic Empire or the Ottoman period, which did occur (giving rise to east Eurasian admixture in Turkey, for example) and may have been more gender balanced.
North Mesopotamia has witnessed dramatic political and social change since the Bronze Age, but the impact of these events on its demographic history is little understood. 
Here we study this question by analysing the recently excavated Late Iron Age settlement of Çemialo Sırtı in Batman, southeast Turkey. Archaeological and/or radiocarbon evidence indicate that the site was inhabited during two main periods: the first half of the 2nd millennium BCE and the first millennium BCE. Çemialo Sırtı reveals nomadic items of the Early Iron Age, as well as items associated with the Late Achaemenid and subsequent Hellenistic Periods. 
Mitochondrial DNA (mtDNA) haplotypes from 12 Çemialo Sırtı individuals reveal high genetic diversity in this population, conspicuously higher than early Holocene west Eurasian populations, which supports the notion of increasing population admixture in west Eurasia through the Holocene. Still, in its mtDNA composition, Çemialo Sırtı shows highest affinity to Neolithic north Syria and Neolithic Anatolia among ancient populations studied, and to modern-day southwest Asian populations. Population genetic simulations do not reject continuity between Neolithic and Iron Age, nor between Iron Age and present-day populations of the region. Despite the region's complex political history and indication for increased genetic diversity over time, we find no evidence for sharp shifts in north Mesopotamian maternal genetic composition within the last 10,000 years.

Note that the "Europe" tag is not because Turkey is in Europe, but because of its relevance to European genetics as a potential place of origin of European population genetics.

Turtle Island


The image above was an unattributed random Facebook meme. Read the first post on the blog, of the same name, to understand the origins of this blog's name.

Wednesday, August 2, 2017

Madagascar's Austronesians and Africans May Not Have Arrived Together

A new study of modern Madgascar's population genetics suggests that the island was first settled by a relatively gender balanced population of Austronesians followed in fairly short order by a male dominated South African Bantu-like population perhaps a century or two later who dominated in coastal areas as the Austronesians took refuge in the highlands. Over time, they then admixed.

Minoan And Mycenaean Ancient DNA

A new paper with Minoan and Mycenaean ancient DNA is out. 

The (non-Indo-European) Minoan individuals have a significant Caucasian component but lack steppe ancestry, as I've suspected for a long time. The Mycenaeans, unsurprisingly for Indo-European migrant/conquerers of the late Bronze Age, have significant steppe ancestry, but somewhat surprisingly, have about 75%-80% ancestry from pre-Myceneaens of the region who tend to resemble the Minoans.

The following quotes from the paper are via Eurogenes who quotes the abstract:
The origins of the Bronze Age Minoan and Mycenaean cultures have puzzled archaeologists for more than a century. We have assembled genome-wide data from 19 ancient individuals, including Minoans from Crete, Mycenaeans from mainland Greece, and their eastern neighbours from southwestern Anatolia. Here we show that Minoans and Mycenaeans were genetically similar, having at least three-quarters of their ancestry from the first Neolithic farmers of western Anatolia and the Aegean [1, 2], and most of the remainder from ancient populations related to those of the Caucasus [3] and Iran [4, 5]. However, the Mycenaeans differed from Minoans in deriving additional ancestry from an ultimate source related to the hunter–gatherers of eastern Europe and Siberia [6, 7, 8], introduced via a proximal source related to the inhabitants of either the Eurasian steppe [1, 6, 9] or Armenia [4, 9]. Modern Greeks resemble the Mycenaeans, but with some additional dilution of the Early Neolithic ancestry. Our results support the idea of continuity but not isolation in the history of populations of the Aegean, before and after the time of its earliest civilizations.
And, a bit of the body of the paper:
The simulation framework also allows us to compare different models directly. Suppose that there are two models (Simulated1, Simulated2) and we wish to examine whether either of them is a better description of a population of interest (in this case, Mycenaeans). We test f4(Simulated1, Simulated2; Mycenaean, Chimp), which directly determines whether the observed Mycenaeans shares more alleles with one or the other of the two models. When we apply this intuition to the best models for the Mycenaeans (Extended Data Fig. 6), we observe that none of them clearly outperforms the others as there are no statistics with |Z|>3 (Table S2.28). However, we do notice that the model 79%Minoan_Lasithi+21%Europe_LNBA tends to share more drift with Mycenaeans (at the |Z|>2 level). Europe_LNBA is a diverse group of steppe-admixed Late Neolithic/Bronze Age individuals from mainland Europe, and we think that the further study of areas to the north of Greece might identify a surrogate for this admixture event – if, indeed, the Minoan_Lasithi+Europe_LNBA model represents the true history.
Lazaridis, Mittnik et al., Genetic origins of the Minoans and Mycenaeans, Nature (August 2, 2017), doi:10.1038/nature23310 (closed access).

Razib Khan provides some nice historical context.

At least one of the Minoans had Y-DNA J2a1h-M319, a Y-DNA type common in the highlands of Anatolia, the Caucasus and Iran. Per Razib: "the authors note that the Y chromosomes in four out of five individuals in their Mycenaean-Minoan-Anatolians are haplogroup J associated with these eastern groups [i.e. early Caucasian and Iranian farmers], rather than the ubiquitous G2 of the earlier farmer populations." There are two J2a1 Minoans (one is J2a1/mtDNA H, and the other one is J2a1d/mtDNA H13a1), one G2a2b2 Minoan (mtDNA U3b3), one J1a Anatolian (mtDNA H) and one J2a1 Mycenaean (mtDNA X2). Two other Mycenaeans are mtDNA X2 with no Y-DNA.

Like the Minoans "they did not find much steppe ancestry in the Anatolian samples at all." Probably the majority view among linguists is that the Anatolian languages were the first to break off from proto-Indo-European, a linguistic conclusion that the authors struggle to reconcile with this fact (they suggest that the lack of steppe ancestry in Anatolia could be due to thousands of years of dilution with local Anatolian gene pools).

But, I have long maintained, based upon historical accounts and archaeological evidence, that the early Hittites were very new arrivals in Anatolia ca. 2000 BCE. In my view the Anatolian languages seem much different than other contemporaneous Indo-European languages not because they broke off from proto-Indo-European languages earlier, but because the Anatolian-Minoan languages that formed the substrate influencing the Hittite languages as they grew distinct from proto-Indo-European was much different from the substrate encountered by proto-Indo-Europeans elsewhere, resulting in a greater divergence from its contemporaneous sister languages.

More worthwhile observations from Razib:
On the one hand Basques seem to have mostly Indo-European Y chromosomes, but their whole genome ancestry indicates less exogenous input than their neighbors. Speaking of which, we know by the Classical period large regions of western Spain were dominated by Celtic speaking peoples, but the genetic imprint of the Indo-Europeans is still very modest in the Iberian peninsula. 
I think what we’re seeing here is the difference between Indo-European agro-pastoralists arriving to a landscape of relatively simple societies with more primal institutions, and those who migrated into regions where local population densities are higher and social complexity is also greater. This higher social complexity means that external elites can takeover a system, as opposed to an almost animal competition for resources as seems to have occurred in Northern Europe.
This new ancient DNA tends to supports the linguistic hypothesis that the Minoan language and the pre-Hittite non-Indo-European languages of Anatolia are part of the same language family as the Caucasian languages. It also supports the idea that Minoan culture is derived proximately from Anatolia.

Probably, the first wave Neolithic ancestry that makes up 75% of the Minoans was the original substrate. This was probably updated with an Enolithic or early Bronze Age migration of Caucasian derived populations across Anatolia to Crete (and more broadly to all of Greece), resulting in substantial introgression of the Caucasian component into the Aegean populations. This introgression that was probably bigger than it seems, because the Anatolian sourced populations who wound up in Crete and became Minoans were probably already admixed in Anatolia with people genetically very similar to the pre-Minoan Greeks, it could very well have been a 50-50 split of newcomers and pre-existing Neolithic populations. Then, the Mycenaeans arrived and provided most of the steppe ancestry present in Greek today early on, although there was moderately more dilution later of the pre-Mycenaean substrate later on.

It appears that genetically Minoan-like people were present throughout the Aegean Sea region of Greece, and not just on Crete where the Minoan palace culture reached its apogee. 

In the dog that didn't bark department, it is also notable that neither the Minoans nor the Mycenaean populations had any more than trace ancestry that looked Levantine or Egyptian, despite the proximity of those civilizations to Greece and the existence of trade exchanges between the Minoans and Mycenaeans and these civilizations.

This doesn't connect all of the dots when it comes to Minoan mysteries. Most importantly, we don't know yet if it is likely that any populations west of the Aegean Sea received genetic contributions from the Minoans. But, it is definitely progress.

Bell Beaker blogger notes some scholarship in the comments at Eurogenes on this final points:
Two fairly short but dense papers: 
www.aegeobalkanprehistory.net 
"When the West meets the East: The Eastern periphery of the Bell Beaker Phenomenon and its Relation with the Aegean Early Bronze Age" 
"Seaborne Contacts between the Aegean, the Balkans and the Central Mediterranean in the 3rd Millennium BC - The Unfolding of the Mediterranean World"
Commentator Alogo also notes:
https://www.academia.edu/4057436/_2013_V._Heyd_Europe_2500_to_2200_BC_Between_Expiring_Ideologies_and_Emerging_Complexity._In_The_Oxford_Handbook_of_the_European_Bronze_Age._Ed._by_H._Fokkens_and_A._Harding_Oxford_University_Press_p._47-67
Lots of the underlying data is available in this blog post

Tuesday, August 1, 2017

CMS Observes Higgs Boson Decays To Tau Leptons That Are Exactly As Predicted

Every new month of discoveries makes it that much more clear that the Higgs boson observed at the LHC is consistent with a theoretically predicted Higgs boson of the observed mass in every way.  
A measurement of the coupling strength of the Higgs boson to tau leptons is performed using events recorded in proton-proton collisions by the CMS experiment at the LHC in 2016 at a center-of-mass energy of 13 TeV. The data set corresponds to an integrated luminosity of 35.9 inverse femtobarns. The H to tau tau signal is established with a significance of 4.9 standard deviations, to be compared to an expected significance of 4.7 standard deviations. The best fit of the product of the observed H to tau tau signal production cross section and branching fraction is 1.09+0.27-0.26 times the standard model expectation. The combination with the corresponding measurement performed with data collected by the CMS experiment at center-of-mass energies of 7 and 8 TeV leads to an observed significance of 5.9 standard deviations, equal to the expected significance. This is the first observation of Higgs boson decays to tau leptons by a single experiment.
CMS Collaboration "Observation of the Higgs boson decay to a pair of tau leptons" (August 1, 2017).

The LHC has also ruled out hypothetical two Higgs doublet additional Higgs bosons predicted by supersymmetry over increasingly large mass ranges as a recent experimental result from the ATLAS experiment illustrates.

Experiment after experiment is ruling out beyond the Standard Model physics. And, the power of these observations is greatly underestimated, because in the Standard Model or any plausible extensions of it, everything is related to everything else at a high enough number of loops. You can't have just around the corner superpartners and extra Higgs bosons, without those particles wrecking havoc on the theoretical predictions for slightly lower energy scales and we're just not seeing that at all.

While individual experimental results consistent with the Standard Model don't by themselves rule out particular phenomena conclusively. The failure of experiments to detect strong experimental BSM signals anywhere over a robust panoply of different kinds of experimental methods magnifies the power of the individual results tremendously.

Realistically, we have reached a "new physics" desert that extends for many order of magnitude in energy scale from the electroweak scale where the Standard Model is situated.

At a minimum, there are no new fundamental particles between the top quark mass and masses dozens of times as large or more. Almost surely, there is not a fourth generation of Standard Model fermions. Higher order fundamental bosons are likewise very unlikely up to the many TeV scale.

Not every last mystery of high energy physics has been unraveled yet. Some of the finer points of hadron physics and neutrino physics still need to be worked out.

But, the Standard Model is now UV complete all of the way up to the GUT scale. There are really no HEP phenomena that require new particles or forces to explain. None of the lingering experimental anomalies are so large that they can't be resolved with better data and a minor theoretical insight or two.

Prospects for a GUT or a TOE look pretty bleak for the foreseeable future, but we are about three physical constants short of a complete Standard Model and not unthinkably far from a theory of quantum gravity that can replace dark matter and dark energy, giving us a complete, if ugly, collection of the laws of Nature. It may take more precision measurement to have a whole that is capable of being definitively tied to one particular theory. But, we're getting there.

While HEP experimentation seems to be at something of a dead end, new astronomy data continues to poor in, which makes it possible to distinguish between competing particle dark matter and modified gravity theories and dark energy theories based upon hard data rather than aesthetic concerns.

Cold Dark Matter Again Fails To Reproduce Observations

Even considering baryon effects, cold dark matter models don't match astronomy observations at the scale of galaxies. 
In cosmological N-body simulations, the baryon effects on the cold dark matter (CDM) halos can be used to solve the small scale problems in ΛCDM cosmology, such as cusp-core problem and missing satellites problem. It turns out that the resultant total density profiles (baryons plus CDM), for halos with mass ranges from dwarf galaxies to galaxy clusters, can match the observations of the rotation curves better than NFW profile. In our previous work, however, we found that such density profiles fail to match the most recent strong gravitational lensing observations. 
In this paper, we do the converse: we fit the most recent strong lensing observations with the predicted lensing probabilities based on the so-called (α,β,γ) double power-law profile, and use the best-fit parameters (α=3.04,β=1.39,γ=1.88) to calculate the rotation curves. We find that, at outer parts for a typical galaxy, the rotation curve calculated with our fitted density profile is much lower than observations and those based on simulations, including the NFW profile. This again verifies and strengthen the conclusions in our previous works: in ΛCDM paradigm, it is difficult to reconcile the contradictions between the observations for rotation curves and strong gravitational lensing.
Lin Wang, Da-Ming Chen, Ran Li "The total density profile of DM halos fitted from strong lensing" (July 31, 2017).

As the body text explains:
It is now well established that, whatever the manners the baryon effects are included in the collisionless CDM N-body cosmological simulations, if the resultant density pro- files can match the observations of rotation curves, they cannot simultaneously predict the observations of strong gravitational lensing (under- or over-predict). And for the case of typical galaxies, the reverse is also true, namely, the SIS profile preferred by strong lensing cannot be supported by the observations of rotation curves near the centers of galaxies.
The cold dark matter paradigm has been dead for a while, and each new paper seems to further refute it. This paper comes close on the heels of findings that (1) sterile particle dark matter models, in general, are inconsistent with observation, (2) baryon effects cannot save CDM models when tested using a methodology different than the one in this new paper, and (3) the collision velocities seen in the Bullet Cluster are inconsistent with particle dark matter models. Of course, direct dark matter detection experiments looking for WIMPs continue to come up empty.

In addition to all of these problems generally applicable to Cold Dark Matter, MACHO candidates have also been directly ruled out for much of their parameter space.

Self-interacting dark matter (SIDM) models are likewise very hard to fit to the observational evidence. As a recent paper sums up the situation for SIDM models: "these constraints rule out the entire parameter space where the self-scattering cross section can be relevant for astrophysical systems." Axion-like Fuzzy Dark Matter models are likewise in trouble.

Warm dark matter models aren't quite as deeply in trouble but they have a very narrow remaining parameter space (also here) and share problems common to sterile particle dark matter models and particle dark matter models generally.

Another limitation on fermion particle dark matter parameter space derives from the impact that dark matter particles with certain parameters would have on the temperature of neutron stars, although at least once precise neutron star temperature measurement is necessary before this can be converted into a viable means of dark matter detection.

Modified gravity theories have to be taken seriously at this point primarily because the particle dark matter alternatives are pretty much ruled out by observational evidence. At least some of these modified gravity theories, however, can fit the data in a wide array of circumstances where particle dark matter theories cannot.

A Precision Charm Quark Mass Measurement Revisited

The latest charm quark mass measurement compares to a Particle Data Group evaluation of 1.28 ± 0.03 GeV, which is provided in lieu of the weighted average of 1,274 ± 5 MeV, presumably because the wide scatter of the experimental determinations is too widely scattered to justify such a low margin of error. Both of those values are consistent with this result.
We determine the charm quark mass m̂ c(m̂ c) from QCD sum rules of moments of the vector current correlator calculated in perturbative QCD. Only experimental data for the charm resonances below the continuum threshold are needed in our approach, while the continuum contribution is determined by requiring self-consistency between various sum rules, including the one for the zeroth moment. Existing data from the continuum region can then be used to bound the theoretical error. Our result is m̂ c(m̂ c)=1272±8 MeV for α̂ s(MZ)=0.1182. Special attention is given to the question how to quantify and justify the uncertainty.
Jens Erler, Pere Masjuan, Hubert Spiesberger, "Charm Quark Mass with Calibrated Uncertainty" (July 28, 2017).

This paper is substantially identical to a paper blogged on October 28, 2016 at this blog by the same authors reporting the same result, although the PDG comparisons have changed in the meantime.

The result is robust because it agrees with results obtained using six other methodologies. The authors state that a determination of the bottom quark mass using the same methods is in the works and that they anticipate a margin of error of about 15 MeV for that determination (again, holding the strong force coupling constant fixed at the world average value).

The PDG values and the results from this paper are for the mass of the charm quark as defined in the MS charm quark mass (a bar appears above the "MS" if properly typeset). The value 1.28 ± 0.03 GeV for the MS¯mass corresponds to 1.67 ± 0.07 GeV for the pole mass. These definitional issues are discussed in this prior post at this blog. Definitions are critical because, unlike the top quark, charm quarks are never observed outside a confining hadron.

The current PDG value for the strong force coupling constant at the Z boson mass is 0.1181(11), which is slightly different than the old PDG value of 0.1182(16) value used in this paper, although this illustrates that the error bar for the value at the strong force coupling constant value greatly understates the true uncertainty in this measurement given the combined uncertainty in the charm quark mass measurement and the strong force coupling constant measurement.