Reactor Anomaly Ascribed To Sterile Neutrinos Isn't Real

The apparent reactor anomaly signal of a sterile neutrino is actually due to failure to properly model fission reactions from Uranium-235 and not from a sterile neutrino after all. This is in accord with other recent evidence pointing to the same conclusion. Furthermore, by not just ruling out this hypothesis, but providing an alternative explanation, this paper really puts the nail in the coffin of this idea. And, the lack of a sterile neutrino singlet not only impacts neutrino physics but also removes one of the more plausible dark matter candidates.

The Daya Bay experiment has observed correlations between reactor core fuel evolution and changes in the reactor antineutrino flux and energy spectrum. Four antineutrino detectors in two experimental halls were used to identify 2.2 million inverse beta decays (IBDs) over 1230 days spanning multiple fuel cycles for each of six 2.9 GWth reactor cores at the Daya Bay and Ling Ao nuclear power plants. Using detector data spanning effective 239Pu fission fractions, F239, from 0.25 to 0.35, Daya Bay measures an average IBD yield, σ¯f, of (5.90±0.13)×10−43 cm2/fission and a fuel-dependent variation in the IBD yield, dσf/dF239, of (−1.86±0.18)×10−43 cm2/fission. 

This observation rejects the hypothesis of a constant antineutrino flux as a function of the 239Pu fission fraction at 10 standard deviations. The variation in IBD yield was found to be energy-dependent, rejecting the hypothesis of a constant antineutrino energy spectrum at 5.1 standard deviations. While measurements of the evolution in the IBD spectrum show general agreement with predictions from recent reactor models, the measured evolution in total IBD yield disagrees with recent predictions at 3.1σ. 

This discrepancy indicates that an overall deficit in measured flux with respect to predictions does not result from equal fractional deficits from the primary fission isotopes 235U, 239Pu, 238U, and 241Pu. Based on measured IBD yield variations, yields of (6.17±0.17) and (4.27±0.26)×10−43 cm2/fission have been determined for the two dominant fission parent isotopes 235U and 239Pu. A 7.8% discrepancy between the observed and predicted 235U yield suggests that this isotope may be the primary contributor to the reactor antineutrino anomaly.

F.P. An, et al., "Evolution of the Reactor Antineutrino Flux and Spectrum at Daya Bay" (April 4, 2017).

Pre-Columbian European Admixture In Northern Chile?

It is widely held that, except for migrations from Beringia or Siberia, there was no contact between the Old World and the New World prior to the colonization of North America by the Norse in the late 10th century AD. 

Analyses of 23 ancient American DNA samples reveal, however, the presence of European admixture in a sample taken from a Chinchorro mummy of northern Chile dated to 3972-3806 BC. This discovery implies a more complex history of the peopling of the Americas than previously accepted.

R. Smith, "European Admixture in Chinchorro DNA" (May 1, 2017).

Critical commentary here suggests that the article is unlikely to survive peer review or to be published. The author is known on the Internet as Genetiker. 

Interesting if true, but I'm skeptical of the result, apparently found in just one sample out of 23. This is a very long way from Europe, at around the time that farming had just reached its maximum extent to the Atlantic Coast. The fact that only one in 23 could be recovered suggests that the quality of the one recovered was itself not very good. Contamination of samples seems like a more likely possibility given that it is very hard to come up with any narrative that can explain this data point.

The admixture estimate is more than 30% and less than 40%, which would suggest 3 of 8 great-grandparents were not Amerindian, pushing back a date of migration from Eurasia to North America of those great-grandparents by roughly a century.

This is too recent to plausible pre-date the LGM without leaving a much bigger demographic mark than one ancient DNA sample that leaves no survivors in modern populations. It is too old to be plausible as the result of an intentional global sea voyage. It predates West Eurasian expansion into the Tarim Basin and probable contact with East Asian civilizations by a couple of thousand years. The pottery associated migration across Siberia went the other direction (from East to West).

The Paleo-Eskimo migration which was a genetic source for the Saqqaq, the subsequent Dorset, and the genetically distinctive component of the Na-Dene was around 2400 BCE, which is 1600-1700 years too recent. A variety of other claimed pre-Columbian contacts are even more recent (even an outlier of a claimed New World seed described in India ca. 2000 BCE).

Big Ancient DNA Paper Preprints

The Bell Beaker Behemoth Paper

Overview

The biggest news from the Bell Beaker Behemoth paper is that Iberian Bell Beaker individuals have almost no genetic overlap with central European Bell Beaker individuals.

The Iberians were local Neolithic farmers who evolved in material culture, which was adopted culturally by people with high proportions of steppe ancestry outside of Iberia. 

The non-Iberians had predominantly Y-DNA R1b-S116 and considerable steppe ancestry, with higher levels of hunter-gatherer ancestry than the Iberians and central-Northern European Neolithic ancestors, although proportions of steppe ancestry varied greatly. But, British Neolithic ancestry and Southern French Neolithic ancestry was from Iberia.

Still as Bell Beaker blogger notes in his commentary:

* Beaker appears to have come directly from the Pontic-Caspian steppe while absorbing LBK-like or admixed ancestry. Census estimates and other data supports this.
* Many of their mito-profiles look steppic. . . .
* Skin, eyes and LP basically identical to Yamnaya, changes over time. (Which I still don't get)
* Not a trickle of people. Waves of immigrants first into Europe, then the isles with massive population increases following (older papers below).

The Paper

The Bell Beaker ancient DNA paper is expected here. The abstract is as follows:

Bell Beaker pottery spread across western and central Europe beginning around 2750 BCE before disappearing between 2200-1800 BCE. The mechanism of its expansion is a topic of long-standing debate, with support for both cultural diffusion and human migration. We present new genome-wide ancient DNA data from 170 Neolithic, Copper Age and Bronze Age Europeans, including 100 Beaker-associated individuals. 

In contrast to the Corded Ware Complex, which has previously been identified as arriving in central Europe following migration from the east, we observe limited genetic affinity between Iberian and central European Beaker Complex-associated individuals, and thus exclude migration as a significant mechanism of spread between these two regions. However, human migration did have an important role in the further dissemination of the Beaker Complex, which we document most clearly in Britain using data from 80 newly reported individuals dating to 3900-1200 BCE. 

British Neolithic farmers were genetically similar to contemporary populations in continental Europe and in particular to Neolithic Iberians, suggesting that a portion of the farmer ancestry in Britain came from the Mediterranean rather than the Danubian route of farming expansion. 

Beginning with the Beaker period, and continuing through the Bronze Age, all British individuals harboured high proportions of Steppe ancestry and were genetically closely related to Beaker-associated individuals from the Lower Rhine area. We use these observations to show that the spread of the Beaker Complex to Britain was mediated by migration from the continent that replaced >90% of Britain's Neolithic gene pool within a few hundred years, continuing the process that brought Steppe ancestry into central and northern Europe 400 years earlier.

I. Olalde, et al., "The Beaker Phenomenon And The Genomic Transformation Of Northwest Europe" (May 9, 2017).

This abstract adds surprisingly little to the abstract of a previously announced conference paper by the same authors about which I made a number of observations.

The Y-DNA Results

We determined Y-chromosome haplogroups for the 54 male Beaker-associated individuals (Supplementary Table 3). Individuals from the Iberian Peninsula carried Y haplogroups known to be common across Europe during the earlier Neolithic period such as I2a (n=3) and G2 (n=1) (Supplementary Table 3). In contrast, Beaker-associated individuals outside Iberia (n=44) largely carried R1b lineages (84%), associated with the arrival of Steppe migrants in central Europe during the Late Neolithic/Early Bronze Age. For individuals in whom we could determine the R1b subtype (n=22), we found that all but one had the derived allele for the R1b-S116/P312 polymorphism, which defines the dominant subtype in western Europe today. Finding this early predominance of the R1b-S116/P312 polymorphism in ancient individuals from central and northwestern Europe suggests that people associated with the Beaker Complex may have had an important role in the dissemination of this lineage throughout most of its present-day distribution.

mtDNA Results

The mtDNA Atlas blog notes some of the interesting mtDNA results from today's papers:

-A high frequency of K1(mostly K1c) in Mesolithic Serbia/Romania. Recall that K1b2 was found in Mesolithic Lithuania a few months ago and K1c was found in Mesolithic Greece a few years ago. 

-High frequency U5a and hg I in British Bell Beaker and British Bronze age. Low frequency of H in British Bell Beaker and British Bronze age. 

-High frequency of H1 and K1a in British, Iberian Neolithic. 

-Several examples of H1b in Eastern European Neolithic (Poland, Ukraine). 

-Middle Eastern mHG R0a1 in Bulgarian Yamnaya. This individual genetically clusters between the Middle East and other Yamnaya individuals.   

The British population turnover

our results imply a minimum of 93±2% local population turnover by the Middle Bronze Age (Supplementary Information, section 6). Specifically, for individuals from Britain around 2000 BCE, at least this fraction of their DNA derives from ancestors who at 2500 BCE lived in continental Europe. An independent line of evidence for population turnover comes from Y-chromosome haplogroup composition: while R1b haplogroups were completely absent in the Neolithic samples (n=25), they represent 95% and 75% of the Y-chromosomes in Beaker Complex-Early Bronze Age and Middle Bronze Age males in Britain, respectively (Fig. 3b; Supplementary Table 3).

Pertinent to this finding is another key paper from a couple of years ago cited by Rob in comments at the Bell Beaker blog:

This paper rewrites the early history of Britain, showing that while the cultivation of cereals arrived there in about 4000 cal BC, it did not last. Between 3300 and 1500 BC Britons became largely pastoral, reverting only with a major upsurge of agricultural activity in the Middle Bronze Age. This loss of interest in arable farming was accompanied by a decline in population, seen by the authors as having a climatic impetus. But they also point to this period as the time of construction of the great megalithic monuments, including Stonehenge. We are left wondering whether pastoralism was all that bad, and whether it was one intrusion after another that set the agenda on the island.

Chris J. Stevens and Dorian Q Fuller, Did Neolithic farming fail? The case for a Bronze Age agricultural revolution in the British Isles (January 2, 2015).

Phenotype associated genetics

Derived alleles at rs12913832 (SLC45A2) and rs16891982 275 (HERC2/OCA2), which contribute to reduced skin and eye pigmentation in Europeans, dramatically increased in frequency during the Beaker and Bronze Age periods (Extended Data 277 Fig. 5). Thus, the arrival of migrants associated with the Beaker Complex significantly altered the pigmentation phenotypes of British populations. 

However, the lactase persistence allele at SNP rs4988235 remained at very low frequencies in our dataset both in Britain and continental Europe, showing that the major increase in its frequency in Britain, as in mainland Europe, occurred in the last 3,500 years.

The very late and thus even harder than expected sweep of the lactase persistence allele is very surprising. The widespread assumption was that the selective fitnesses enhancing effect of this gene rode piggyback on the Bell Beaker expansion or even was present in the seed Bell Beaker population from the steppe. This evidence, pretty convincingly, says no. The sweep hasn't even really started as of about 1500 BCE and it wasn't a result of the population replacement in Britain and much of Western Europe with steppe-like people.

Moreover, we know that after 1500 BCE the gene pool of Western Europe was substantially similar to what it is today, although there were differences in detail.* This hard sweep has become even more of a mystery than it was before this study came out. And, this hard sweep had to have been propelled almost entirely by its intrinsic selective fitness enhancing properties without otherwise disrupting the population structure of Europe. It seems likely that there is some unknown phenotypic property of the LP genes which is European specific and incredibly fitness enhancing. My best guess at this point is that the LP gene in pregnant women greatly reduces the odds of miscarriage and lowers infant mortality for their children and greatly reduces maternal mortality because it enhances the health of the pregnant woman.

* As Razib notes:

In the context of this paper the Anglo-Saxon migrations tackled by the PoBI paper are minor affairs because the two populations were already genetically rather close. Additionally, the PoBI paper found that the German migrations were significant demographic events, but most of the ancestry across Britain does date to the previous period.

Razib states that this is consistent with the result in Iain Mathieson, et al., "Eight thousand years of natural selection" (October 10, 2015). That paper says:

The strongest signal of selection is at the SNP (rs4988235) responsible for lactase persistence in Europe. Our data strengthens previous reports that an appreciable frequency of lactase persistence in Europe only dates to the last four thousand years. The allele’s earliest appearance in our data is in a central European Bell Beaker sample (individual I0112) that lived between approximately 2300 and 2200 BCE. 

The frequency of the derived LP gene is currently 75%. It was about 1% in Neolithic Britons and not more than about 5% in the Bell Beaker people.

Razib also notes that there is significant late Bronze Age/post-Bronze Age selection for SLC45A2 (associated with light skin color) and HERC2-OCA2 (associated with blue eyes) in the post-Bell Beaker era of the last 4,000 years, because while the ancestral darker skin, brown eyed versions of these alleles was less common in the steppe folk than in the Neolithic British, the ancestral versions were still much more common then than they are today.

Derived HERC2 was present in about 20% of the Neolithic British, 65% of the Bell Beaker British, and about 80% of the modern British.  About 4% of the Neolithic British had blue eyes. About 45% of the Bell Beaker British had blue eyes. About 64% of the modern British have blue eyes.

SLC45A2 was present in about 25% of the Neolithic British, about 68% of the Bell Beaker British, and about 96% or more of the modern British. (It is 82% in Iberians and a bit lower in Sardinians according to Razib.) More than half of the Neolithic would have been much darker skinned, about one in nine Bell Beaker British would have been much darker skinned, and about one in 2,500 or less of the ancestrally European British are that dark skinned now.  A study from a year ago by Field, et al., finds selection on this gene within the last 2,000 years.

Autosomal genetics

We grouped Beaker Complex individuals based on geographic proximity and genetic similarity (Supplementary Information, section 4), and used qpAdm2 to model their ancestry as a mixture of western European hunter-gatherers (WHG), northwestern Anatolian farmers, and Yamnaya steppe pastoralists (the first two of which contributed to earlier European farmers; Supplementary Information, section 6). 

We find that the great majority of Beaker Complex individuals outside of Iberia derive a large portion of their ancestry from Steppe populations (Fig. 2a), whereas in Iberia, such ancestry is absent in all sampled individuals, with the exception of two (I0461 and I0462) from the Arroyal I site in northern Spain. We detect striking differences in ancestry not only at a pan-European scale, but also within regions and even within sites. Unlike other individuals from the Upper Alsace region of France (n=2), an individual from Hégenheim resembles previous Neolithic populations and can be modelled as a mixture of Anatolian Neolithic and western hunter-gatherers without any Steppe-related ancestry. Given that the radiocarbon date of the Hégenheim individual is older (2832–2476 cal BCE) (quoting 95.4% confidence intervals for this and other dates) (Supplementary Information, section 1) than other samples from the same region (2566–2133 cal BCE), the pattern could reflect temporal differentiation. At Szigetszentmiklós in Hungary, we find Beaker Complex- associated individuals with very different proportions (from 0% to 74%) of Steppe ancestry but  overlapping dates.  . . .

there is genetic affinity to Iberian Early Neolithic farmers in Iberian Middle Neolithic/Copper Age populations, but not in central and northern European Neolithic populations (Fig. 2b), which could be explained by differential affinities to hunter-gatherer individuals from different regions (Extended Data Fig. 2). A new finding that emerges from our analysis is that Neolithic individuals from southern France and Britain also show a greater affinity to Iberian Early Neolithic farmers than to central European Early Neolithic farmers (Fig. 2b), similar to previous results obtained in a Neolithic farmer genome from Ireland. By modelling Neolithic populations and WHG in an admixture graph framework, we replicate these results and further show that they are not driven by different proportions of hunter-gatherer admixture (Extended Data Fig. 3; Supplementary Information, section 5). Our results suggest that a portion of the ancestry of the Neolithic farmers of Britain was derived from migrants who spread along the Atlantic coast. Megalithic tombs document substantial interaction along the Atlantic façade of Europe, and our results are consistent with such interactions reflecting movements of people. . . . .

For Beaker Complex individuals from Iberia, the best fit was obtained when Middle Neolithic and Copper Age populations from the same region were used as a source for their Neolithic farmer-related ancestry, and we could exclude central and northern European populations (P < 4.69E-03) (Fig. 2c). Conversely, the Neolithic farmer-related ancestry in Beaker Complex individuals outside Iberia was most closely related to central and northern European Neolithic populations with relatively high hunter-gatherer admixture (e.g. Globular_Amphora_LN, P = 0.14; TRB_Sweden_MN, P = 0.29), and we could significantly exclude Iberian sources (P < 3.18E-08) (Fig. 2c). These results support largely different origins for Beaker Complex individuals, with no discernible Iberia-related ancestry outside Iberia. 

Data From The Portugal Paper

Another ancient DNA from Portugal paper also came out today:

We analyse new genomic data (0.05-2.95x) from 14 ancient individuals from Portugal distributed from the Middle Neolithic (4200-3500 BC) to the Middle Bronze Age (1740-1430 BC) and impute genomewide diploid genotypes in these together with published ancient Eurasians. 

While discontinuity is evident in the transition to agriculture across the region, sensitive haplotype-based analyses suggest a significant degree of local hunter-gatherer contribution to later Iberian Neolithic populations. A more subtle genetic influx is also apparent in the Bronze Age, detectable from analyses including haplotype sharing with both ancient and modern genomes, D-statistics and Y-chromosome lineages. However, the limited nature of this introgression contrasts with the major Steppe migration turnovers within third Millennium northern Europe and echoes the survival of non-Indo-European language in Iberia. 

Changes in genomic estimates of individual height across Europe are also associated with these major cultural transitions, and ancestral components continue to correlate with modern differences in stature.

Rui Martiniano, et al., "The Population Genomics Of Archaeological Transition In West Iberia"(May 10, 2017).

Linguistic Implications

The hypothesis that Vasconic languages, of which the last survivor is Basque, is derived from a language of the first farmers of Iberia, or maybe even remotely possibly a Mesolithic language of the Franco-Cantabrian refuge, looks stronger than it did yesterday. 

These discoveries also cast doubt on the linguistic character of non-Iberian Bell Beaker people. Yes, there was a definite shift to Bell Beaker relics, but was this accompanied by language shift, or not? 

Of course, even if they did speak Indo-European languages, this still doesn't solve the problem that the Celtic language family is too young to have arrived ca. 2500 BCE to 2000 BCE, when the population turnover took place and there was no doubt language shift of some kind in the British Isles and much of the rest of Western Europe accompanying a 91%-95% population turnover.

The Southeast European Ancient DNA Paper

The genomic history of Southeast Europe is expected here. The abstract is as follows:

Farming was first introduced to southeastern Europe in the mid-7th millennium BCE - brought by migrants from Anatolia who settled in the region before spreading throughout Europe. However, the dynamics of the interaction between the first farmers and the indigenous hunter-gatherers remain poorly understood because of the near absence of ancient DNA from the region. We report new genome-wide ancient DNA data from 204 individuals-65 Paleolithic and Mesolithic, 93 Neolithic, and 46 Copper, Bronze and Iron Age-who lived in southeastern Europe and surrounding regions between about 12,000 and 500 BCE. 

We document that the hunter-gatherer populations of southeastern Europe, the Baltic, and the North Pontic Steppe were distinctive from those of western Europe, with a West-East cline of ancestry. 

We show that the people who brought farming to Europe were not part of a single population, as early farmers from southern Greece are not descended from the Neolithic population of northwestern Anatolia that was ancestral to all other European farmers.  

The ancestors of the first farmers of northern and western Europe passed through southeastern Europe with limited admixture with local hunter-gatherers, but we show that some groups that remained in the region mixed extensively with local hunter-gatherers, with relatively sex-balanced admixture compared to the male-biased hunter-gatherer admixture that we show prevailed later in the North and West. 

After the spread of farming, southeastern Europe continued to be a nexus between East and West, with intermittent steppe ancestry, including in individuals from the Varna I cemetery and associated with the Cucuteni-Trypillian archaeological complex, up to 2,000 years before the Steppe migration that replaced much of northern Europe's population.

I. Mathieson, et al., "The Genomic History Of Southeastern Europe" (May 9, 2017).

Hat tip for the links to Eurogenes, and to Razib for the strong hint that they are coming this week.

The Evolution Of Lactase Persistence

UPDATE: The Bell Beaker Behemoth paper data casts grave doubt on the conjectures made in this paper about the LP gene's source, means of expansion, and fitness effects.

Lactase persistence-the ability of adults to digest the lactose in milk-varies widely in frequency across human populations. This trait represents an adaptation to the domestication of dairying animals and the subsequent consumption of their milk. Five variants are currently known to underlie this phenotype, which is monogenic in Eurasia but mostly polygenic in Africa. 

Despite being a textbook example of regulatory convergent evolution and gene-culture coevolution, the story of lactase persistence is far from clear: Why are lactase persistence frequencies low in Central Asian herders but high in some African hunter-gatherers? Why was lactase persistence strongly selected for even though milk processing can reduce the amount of lactose? Are there other factors, outside of an advantage of caloric intake, that contributed to the selective pressure for lactase persistence? It is time to revisit what we know and still do not know about lactase persistence in humans.

Segurel and Bon, "On the Evolution of Lactase Persistence in Humans." 18 Annual Rev Genomics Hum Genet. (April 19, 2017 [Epub ahead of print which is anticipated on August 31, 2017]).

Hat tip to Bell Beaker blogger.

The Conventional Wisdom

LP genes are rare in the first farmers of Europe, but become present at a very high frequency in Western Europe around the time of the Bell Beaker expansion. Conventionally, it has been assumed that the European LP variant evolved in situs in Northwest Europe in the Late Neolithic/Early Bronze Age and increased rapidly in frequency because it conferred greater selective fitness. 

Two Reasons To Doubt The Conventional Wisdom

But, two things have cast doubt on the conventional wisdom. 

First, it has become clear that the Bell Beaker expansion and Corded Ware Expansion both involved, at about the same time, massive migration and at least significant partial replacement of existing populations with people who have significant ultimate European steppe pastoralist ancestry. 

This migrationist reinterpretation of the Bell Beaker phenomena implies that it is possible that an LP gene already present at reasonably high frequencies in the steppe ancestors of these people may have ridden piggy back on the selective fitness advantages associated with being part of a Bronze Age technology, dairying civilization. These people had huge cultural advantages that conferred selective fitness among people who use stone tools, who were ancestrally farmers whose food production methods have experienced a collapse, who used cattle primarily as a labor source and source of meat. These cultural advantages may not have been instrumentally related to their LP phenotype. A small part of the rise in LP frequency may have involved instrumental benefits associated with this gene, but mostly it is a marker for being in a more technologically advanced culture that is growing in market share and absolute numbers in Western Europe.

The extreme growth in LP frequencies in this time period in Europe, in other words, looks a lot like it was driven to a significant extent by a founder effect that takes hold right at the bottom of one of the most severe bottlenecks in European population history. Note also that if the subset of the population driving the expansion of the Bell Beaker culture across Western Europe had significantly higher than average levels of the LP gene due to random chance, relative even to the population in which Bell Beaker ethnogenesis occurred, this founder effect could be particularly strong.

For example, suppose that Bell Beaker ethnogensis occurred in Iberia ca. 2800 BCE when three hundred pre-Bell Beaker men and thirty pre-Bell Beaker women migrate there with most of the pre-Bell Beaker men marrying local women, and that 30% of the resulting Proto-Bell Beaker people in Iberia have the LP gene. But, suppose that 80% of the expansion of the Proto-Bell Beaker culture into Western Europe arises from 20% of the Proto-Bell Beaker population and that 70% of the people in this rapidly expanding subset of Proto-Bell Beakers have the LP gene. In a scenario where there is near total replacement of the prior first wave Neolithic population with expanding Bell Beaker people as there was in England, the frequency of the LP gene could go from nearly zero, to more than 60%, extremely rapidly, even in the LP gene, instrumentally had no selective fitness benefits. 

If the LP gene had at least some modest instrumental selective fitness benefits (which seems much more plausible than the conventional wisdom in which it is a decisive factor in likelihood of survival all by itself), it might easily rise in frequency in Eastern Europe to 65% to 70% over the 40 to 60 generations during which the Bell Beaker culture endured relative to the baseline 60% frequency it would have had if it was ancestrally informative but selectively neutral. A shift from 60% to 67.5% over 50 generations (i.e. about 0.15 percentage points per generation on average) looks a lot less impressive than a shift from less than 1% to 60% to 70% over 65 or so generations (i.e. 1 percentage point per generation on average).

Of course, this only works if the steppe population ancestral to the pre-Bell Beaker migrants had some appreciable level of the LP gene developed over many generations in a resource poor steppe pastoralist context where the adult LP phenotype might have had greater selective fitness benefits than it did in Bronze Age Western Europe by about 3000 BCE. So far as I know, there is not much ancient DNA evidence to support this hypothesis, yet, but not enough data to rule out this very plausible hypothesis either. 

If this is how the LP gene came to be so common in Western Europe, it also provides another line of evidence strongly disfavoring an ancestral origin of the pre-Bell Beaker people linked to pastoralists in North Africa (such as Nilo-Saharan peoples) where different LP genes arose than the one that is the predominant source of the LP phenotype in Europe.

N.B. These percentages are merely gross estimate place fillers used to illustrate the concept and not actually documented historical percentages (apart from the less than 1% frequency of the LP gene pre-Bell Beaker).

Second, the increase in the frequency of the LP gene is so great, over so short a time period in the ancient DNA record that it is hard to imagine any realistic scenario that would give it such an intense selective fitness enhancing effect - pretty much unrivaled in the history of human evolution.

Death from insufficient caloric intake is primarily a scourge of young children who can drink cow's milk whether or not they have the LP gene which only impacts ability to drink milk without incident as an adult. Immune benefits associated with vitamin D may be real but vitamin D deficiencies (which are a particularly issue in higher latitudes) aren't that huge of a mortality risk inducing factor these days in adults, although infectious diseases were definitely a much bigger mortality risk from the Neolithic era right into the early 19th century, than they are today, even among adults, although most infectious disease deaths historically also involved children for whom the European LP gene should be irrelevant.

Also, as the article notes, since foods like cheese and yogurt that make dairy products usable for adults who lack the LP phenotype were made as far back as the early Neolithic, it is hard to see why avoiding this modest food processing burden would have such a huge effect on the mortality rates of adults in the Bronze Age.

Nobody doubts that the LP phenotype enhances selective fitness at the margin, but it just doesn't make sense that it should be the most fitness enhancing trait there ever was unless it repelled some virulent pathogen that was as deadly to adults as it was to children which evolved in parallel to become far less deadly to adults even in the absence of LP over the next 1,500 to 1,000 years.

In contrast, it is easy to see how the membership in a culture whose package of comparatively advanced technologies and perhaps also forms of social organization brought by the Bell Beaker people to Western Europe in  this time period could confer extremely enhanced selective fitness.

Historical Narratives That Explain The Seeming Paradoxes

This isn't necessarily inconsistent with the low levels of LP gene frequency in Central Asian populations today. The LP phenotype is rare in Eastern Asia and Central Asia's demographics have been heavily influenced by multiple waves of Altaic migration from the East in the last couple of thousand plus years - first by linguistically Turkic populations and then by the Mongolia Empire. And, in these East Asian pastoralist cultures, the horse was more central than the cow, for example, with fermented horse milk as a culturally important drink. So, even if Central Asia had high levels of the LP gene when it was filled with people who were mostly ancestrally West Eurasian, those levels may be low now due to a population turnover in favor of ancestrally East Eurasian people. Empirically, there is a pretty gradual cline in relative shares of East Eurasian and West Eurasian ancestry along the historic Silk Road today.

In Africa, different LP genes evolved more or less independently of those in Europe, especially in pastoralist Nilotic populations, and there has been more introgression of genes from pastoralist Nilotic populations into hunter-gatherer populations than the other way around, and has been more of an exchange of genes between Nilotic pastoralists and hunter-gather populations whose ways of life and world views are more similar to each other, than there has been between sedentary farmers and hunter-gatherers whose lifestyles and world views are more disparate. So, it makes sense that African hunter-gatherers currently have significant frequencies of LP genes even though this adds little selective fitness in a culture that does not keep dairy cows and does not buy cow's milk for adults in large quantities from cultures that do.

There Are No Black Holes In The LHC

The CMS experiment looked for black holes at the Large Hadron Collider (LHC) in a search including higher energy Run-2 data, and found none. As a result, CMS has excluded the possibility that black holes could be created by high energy particle collisions such as those produced by LHC Run-2, up to extremely high energies.

A search for new physics in energetic, high-multiplicity final states has been performed using proton-proton collision data collected with the CMS detector at a center-of-mass energy of 13 TeV and corresponding to an integrated luminosity of 2.3 inverse femtobarns. The standard model background, dominated by multijet production, is determined exclusively from control regions in data. No statistically significant excess of events is observed. 

Model-independent limits on the product of the cross section and the acceptance of a new physics signal in these final states are set and further interpreted in terms of limits on the production of black holes. Semiclassical black holes and string balls with masses as high as 9.5 TeV, and quantum black holes with masses as high as 9.0 TeV are excluded by this search in the context of models with extra dimensions, thus significantly extending limits set at a center-of-mass energy of 8 TeV with the LHC Run 1 data.

CMS Collaboration, "Search for black holes in high-multiplicity final states in proton-proton collisions at sqrt(s) = 13 TeV" (May 3, 2017).

The 9.0 TeV exclusion of quantum black holes is equivalent to a 9,000,000 MeV exclusions.

By comparison, an electron is 0.511 MeV, a proton is 938.2 MeV, a neutron is 939.6 MeV, a tau lepton is about 1,776 MeV, the pole mass of a bottom quark is about 4,200 MeV, a Higgs boson is about 125,090 MeV and the pole mass of a top quark is about 174,000 MeV. 

This is the mass of a complex organic molecule, or several dozen uranium atoms.

Conference Abstract Re Big Bell Beaker Paper Released

The first hints about the Bell Beaker Behemoth paper are out, in the form of a conference presentation abstract predating the release of the paper itself (which may be out by the time that the conference presentation is delivered). It answers some questions (mostly in ways we would expect) while leaving the answers to lots of other key questions under answered. Via Eurogenes (emphasis and paragraph breaks mine). Razib's first take on the abstract is here.

The Bell Beaker Complex (BBC) was the first widely distributed archaeological phenomenon of western Europe, arising after 2800 BCE probably in Iberia and spreading to the north and east before disappearing at the latest by 1800 BCE. An open question is the extent to which the cultural elements associated with the BBC spread through movement of ideas or people. 

We present new genome-wide DNA data from 196 Neolithic and Bronze Age Europeans – the largest report of genome-wide data in a single study to date – and merge it with published data to form a dataset with 109 BBC individuals that provides a genomic characterization of the BBC across its geographic and temporal range. 

In contrast to people of the Corded Ware Complex who were partly contemporaries of the BBC in central and eastern Europe and who brought steppe ancestry into central Europe through mass migration and replacement of local populations, we show that the initial spread of the BBC into central Europe from the Iberian Peninsula was not mediated by a large-scale migration but rather through communication of ideas. 

However, the further spread of the BBC beyond central Europe did involve mass movement of people. Focusing on Britain, which includes 81 of our new samples in a time transect from 3900-1300 BCE, we show that the arrival of the BBC around 2400 BCE was mediated by migration from the continent: British individuals associated with Beakers are genetically indistinguishable from continental individuals associated with the same material culture and genetically nearly completely discontinuous with the previously resident population. Such discontinuity persists through to samples from the Bronze Age, documenting a demographic turnover at the onset of the Bronze Age that was crucial to understand the formation of the present-day British gene pool. The arrival of the BBC in Britain can thus be viewed as the western continuation of the massive movement of people that brought the Corded Ware Complex and steppe ancestry into central Europe a few hundred years before.

Olalde, Reich, et al., "Western Europe during the third millennium BCE: A genetic characterization of the Bell Beaker Complex," AetG17 abstracts

Reactions

* Coming Soon. A comment at the Bell Beaker blogger blog provides some insight on when the paper itself will become available. Craig Faber says (emphasis added):

Iñigo Olalde and David Reich are doing a presentation at a workshop at Kiel University that runs from May 17 to 22. Their presentation will focus on population turn-over in Britain associated with the arrival of the Bell Beaker phenomenon there, using new data from Britain, and new and previously published aDNA from other countries for comparison.

The main news here, I think, is that results from the Behemoth study are currently embargoed till publication, and, by the time of the workshop, they no longer will be. The abstract for Reich and Olalde's upcoming presentation in Kiel provides no insight into what was going on in Iberia and Ireland in the same time period, but the Behemoth paper itself probably will (and hopefully they'll have some data from France as well). That's my take on this anyway.

* Dates. The beginning dates in Iberia and Britain sound about right. I would have put the end of the Bell Beaker period in Western Europe at 1300 BCE to 1200 BCE. The distinction matters quite a bit for linguistics purposes and in analyzing the cause of the Bell Beaker decline. Of course, part of the issue is which archaeological cultures to treat as Bell Beaker derived.

* Linguistic Speculation. The Abstract Is Silent On Language. The authors have interestingly backed away from the linguistic claims that were a source of great dispute within their group in their last paper. This is appropriate. The evidence regarding Bell Beaker historical linguistics is much less clear. But, certainly, one would not expect a population engaged in mass folk migration to experience language shift. 

Has There Been A Struggle Over Data Interpretation? One of my theories on why the Bell Beaker Behemoth paper has taken so long to get into print after the data was available but embargoed is that there has been infighting, again, over how strong a statement to make about the linguistic implications of the genetic data. My take would be that this abstract suggests that the "avoid making linguistic claims" camp has largely won the battle. Perhaps those who wish to make linguistic claims will publish separate satellite papers (maybe even advancing competing theories). 

The Indo-European Scenario. If the Bell Beaker people spoke an Indo-European language, you'd expect it to be an early version of Celtic. But, the Celtic language family seems far too young, unless you have a phenomena like the Romance languages where the Bell Beaker languages were homogenized at the peak of the Bell Beaker era though long distance migration and only started to form regional dialects (a la the post-Latin Romance languages) when the Bell Beaker phenomena collapsed. In this scenario, the Basque people and related languages that went extinct just at the dawn of attested history nearby, where a case of Indo-Europeans of a Celtic persuasion experiencing language shift and religion shift to a pre-existing first farmer language and faith, perhaps due to high levels of intermarriage with local Iberian women in a male dominated migration. 

The Non-Indo-European Scenario. But, that scenario is hard to reconcile with the likely origins of the modern Basque not in a migration direct from Southern Portugal where the Bell Beaker phenomena began ca. 2800 BCE, but indirectly from Bell Beaker people who migrated to France and then migrated again to Northern Iberia and Southwest France. Why would language shift happen in Iberia after migrations to France and Britain have already happened?

I Still Think The Non-Indo-European Scenario Is More Probable. In my view the weight of the evidence still supports a non-Indo-European linguistic character for the Bell Beaker people followed by language shift to Celtic languages with only a modest demic component around the time of Bronze Age collapse. Of course, if non-Indo-European Bell Beaker people and Indo-European pre-Celtic and Celtic people ca. 1300 BCE to 500 BCE were very similar in autosomal genetics (and maybe even in mtDNA drawn from related first farmer maternal gene pools enriched in mtDNA H for some reason), it might be easy to underestimate the demic impact of the Bronze Age collapse Indo-Europeans, particularly if some were Bell Beaker Y-DNA R1b men who had been converted culturally to Indo-Europeans while only most were Corded Ware Culture Y-DNA R1a men.

* Central Europeans. It isn't too surprising that areas on the fringe of the Bell Beaker area do not primarily involve demic migration, although it would be interesting to see if there are at least Y-DNA haplogroups or a superstrate percentage of Bell Beaker autosomal genetics. Are Bell Beaker autosomal components at all distinguishable from Corded Ware Culture autosomal components? Did material culture shift in Central Europe also involve a religion and/or language shift? Was it imposed by a thin superstrate or willingly adopted via trade and missionaries as early Bell Beaker theories assumed?

* British Population Replacement. Significant replacement in Britain was foreshadowed by previous results. Other sources have indicated that the First wave Neolithic farmers in England (who arrived, if I recall correctly, around 4000 BCE, had pretty much reverted to hunting and gathering by the time that the Bell Beaker people arrived. I'm curious to know what percentage of the population was replaced and what the gender balance of that replacement was, although a lot (including regional variation in the patterns) can be inferred from existing current British genetics. 

Was Bell Beaker the last big shakeup in British population genetics? It seems as if this was the last really major change in British population genetics with Bronze Age collapse and the arrive and departure of Roman rule having only a modest effect, although some fairly faint Anglo-Saxon and Norman signals seem to be visible in modern British population genetics - of course, given that the putative source of those signals and the putative recipients of them weren't all that different genetically due to the Bell Beaker replacement from more or less the same region ca. 2400 BCE, it isn't too surprising that it is hard to see. I'm also a bit surprised that there isn't an easily visible Punic genetic component in coastal Britain and Ireland, although perhaps it is so consistent across maritime Western Europe in general that it can't be distinguished.

* What About Western Europe? Very little is said about Bell Beaker genetics in Western Europe, despite the centrality of Iberia, France and the Benelux countries to that phenomena.

* What About Lactase Persistence? It would be interesting to know about LP genes over the long transect of time. Was it there from the start or was this a period of active fitness based selection.

* Are Bell Beaker People Just CWC People With Bows And Different Pottery Tastes? Reich's parting sentence suggests that British Bell Beaker people were very similar Corded Ware Complex and Pontic-Caspian steppe people in autosomal genetics. 

Is there any genetic evidence for a male dominated migration from the steppe to Iberia, followed by a new ethnogenesis of the Bell Beaker culture, followed by a secondary expansion?

* By what route to steppe derived Bell Beaker genetics arrive? Slow By Land Or Fast Possibly By Sea? There seems to be a fair amount of Y-DNA R1b phylogeny and modern European Y-DNA R1b haplogroup distribution evidence to support a gradual expansion path of people with Y-DNA R1b and presumably also autosomal steppe ancestry from the steppe to Central Europe and the radiating from there. But, the archaeology and mtDNA seems to support a rapid long distance migration of men with Y-DNA R1b and steppe autosomal genetics to Iberia from Eastern Europe, perhaps by sea, followed by secondary expansion from Iberia as explained in the introductory sentence of the abstract. What can explain this disparity?

Centuries Of Folk-Migration Pre-Ethnogenesis? One conceivable theory would by a 300 years in the wilderness scenario in which a bunch of displaced steppe men seeking their fortunes with Y-DNA R1b (perhaps defeated Yamnaya men) migrate and leave descendants in central Europe (perhaps as wandering raider bands a la the Goths and the Vandals) and then radially until they reach Iberia, but that they don't thrive until they arrive in Portugal which has the metal resources they need, at which point there is Bell Beaker ethnogenesis, possible language shift, and rapid secondary expansion.

Razib Khan makes a similar point about complex models involving potential secondary expansions at his blog:

It would not be entirely surprising if the originators of a cultural complex transmitted it to another group, and then that culture “hitchhiked” on the demographic expansion of the receiving group. A good example would be Roman Catholic Christianity. The Iberians spread it to the New World, along with substantial demographic movement. But the religion itself did not spread to Iberia through migration, but rather cultural shift.

The reference in his post to the Milesians is presumably the the Greek philosophers from Ionia on the Western Coast of Anatolia who brought about a major worldview change in Greek thought in the 6th century BCE (although arguably in that case for the worse). By implication, he suggests that the new paper of Reich and company will change the paradigms of European prehistorians for many years to come with their ancient DNA data as they have already started to do with their Indo-Europeans from the Steppe paper. 

Hiding In Plain Sight

If the Younger Dryas climate event was caused by fragments of comets hitting North America around 10890 BCE (a theory which looks increasingly convincing), where are the craters?

This is a question that its proponents largely leave unanswered.

Short Answer

The obvious answer is that they are hiding in plain sight.

The Great Lakes and a group of three Lakes in the Northwest Canada look like plausible candidates for Younger Dryas Impact craters. 

Most of the Great Lakes are obvious good fits for this hypothesis due to features that make them unique in the world as are a couple of the Northwest Canadian Lakes. They are very deep and large where their conventional creation stories do not provide compelling support for either of these features, in the right place in North America beneath the former Laurentide Ice Sheet. Both groups of lakes were "born" in the Younger Dryas.

In the Northwest Canada case and the Lake Erie cases, an analysis of how the lakes have evolved from Younger Dryas era Paleo-Lakes which were quite different from those we observe today makes the case clearer. 

The three lakes in the Northwest Canada are derived from a single historic Lake Peace that came into being around the time of the Younger Dryas. Lake Erie was more than three times as deep as it is today at the time of the Younger Dryas, but then was filled with sediment.

One can easily imagine a 1000 meter asteroid or comet fragment breaking into two pieces, the smaller of which on a more directly downward angle formed ancient Glacial Lake Peace, and the larger of which after fragmenting further close to the point of impact at more of an angle to the surface of the Earth, formed the predecessors to today's Great Lakes.

Note On The Younger Dryas Impact Theory

An ancient temple in South-Central Turkey (putting a date stamp on the event with pictograms that correspond to historical astronomy) and Hopi legends (about the end of the first world in fire plunging them into a cold era interpreted likewise here) both tend to corroborate this theory as does physical evidence of impact debris in North America, and astronomy evidence. The sudden onset and relatively short duration of this severe climate event also tend to corroborate the theory, although other options related to a disruption of Atlantic Ocean currents by glacial meltwater have been proposed but not directly confirmed.

Determining exactly why and how the climate impacts of the Younger Dryas transpired isn't simply a matter of historical interest. This event is one of the best available proxies for how global climate behaves in periods of abrupt change that serves as source data for models interpreting how human air pollution is leading to global warming. And, if we misinterpret what was going on in the Younger Dryas, our climate models may also be less accurate than they could be with a more accurate analysis.

The Younger Dryas had a global impact, for example, giving rise to a severe drought in Southern Taiwan.