Sardinian Population Genetics

Why Care About Sardinian Genetics?

The population genetics of Sardinia are notable mostly because it is the population that is the closest modern match to the population genetics of the Neolithic era first farmers of Europe. 

In large part because it was an island in the relatively warm Mediterranean sea, it was basically unpopulated prior to the Neolithic Revolution, and experienced far less Middle Neolithic to Early Bronze Age change in its populations than Continental Europe, due to migration from the Steppe. 

This was from both Indo-European initially in the form of the Corded Ware Culture, from the Bell Beaker culture (of uncertain linguistic affiliation) and from later linguistically Indo-European and Uralic migrations into Europe. 

Findings Of The New Large Sample Size Study

A new study with a larger sample size than its predecessors has found that the mountainous regions of the island have been particular stable population genetically since it was settled by first wave farmers of the Neolithic era. 

As in most cases in Europe, new migration to Sardinia from the mainland appears to have been male biased, even before the Bronze Age.

Why Is There A Basque Affinity In Sardinian Population Genetics?

It isn't entirely clear if the stronger genetic affinity of this Sardinian highlands population to the Basque population is due to a greater proportion of hunter-gatherer and Neolithic ancestry, or is due to demic Bell Beaker impacts on Sardinia. 

One way to model the population genetics of Western Europe is to see four primary layers: a Mesolithic layer of Western European hunter-gatherers, a first wave Neolithic farmer layers, a Bell Beaker layer (dating to the early Bronze Age), and an Italo-Celtic-Germanic Indo-European layer (dating to the early Iron Age). 

In this model, the Basque have contributions from the first three layers, while the rest of Western Europe has contributions from all four layers. A reduced "Bronze Age Steppe" component in Sardinians and Basque people could reflect the absence of the fourth layer but not the third, or could reflect a reduced third and fourth layer contribution.

This study, however, does not appear to really consider this possible model and instead assumes three layer model without distinct Bronze Age and Iron Age Steppe migrations, even though the Y-DNA data seems to support such a model.

The body of the paper states regarding the Basque affinity:

Due to its smaller long-term effective population size (Figure 5A), Sardinia is expected to have undergone accelerated rates of genetic drift. To correct for this when measuring similarity to other mainland populations, we used “shared drift” outgroup-f3 statistics (Raghavan et al. 2014), which are robust to population-specific drift. Using this metric, we find the Basque are the most similar to Sardinia, even more so than neighboring mainland Italian populations such as Tuscany and Bergamo (Figure S6A, S6B). 

This relationship is corroborated by identityby-descent (“IBD”) tract length sharing, where among mainland European populations, French Basque showed the highest median length of shared segments (1.525 cM) with Arzana (Figure S7). 

We also tested the affinity between Sardinians and Basque with the D-statistics of the form D(Outgroup, Sardinia; Bergamo or Tuscan, Basque). In this formulation, significant allele sharing between Sardinia and Basque, relative to sharing between Sardinia and Italian populations, will result in positive values for the D-statistic. We find that Sardinia consistently showed increased sharing with the Basque populations compared to mainland Italians (|Z|> 4; Figure S6C), and the result was stronger when using the Arzana than Cagliari sample (DARZ = 0.008 and 0.0096, DCAG = 0.0072 and 0.0087 for French Basque and Spanish Basque, respectively). In contrast, sharing with other Spanish samples in our dataset was generally weaker and not significant ( |Z| < 3.5; Figure S6C), suggesting the shared drift with the Basque is not mediated through Spanish ancestry. . . . 

We generally find that Sardinians have the highest observed levels of shared drift with early Neolithic farming cultures and low levels of shared drift with earlier hunter-gather samples (Figure 6A, Figure S9, Table S5), consistent with previous reports. Surprisingly though, when examining allele sharing within Sardinia, we found that both ancient Neolithic farmer ancestry and pre-Neolithic ancestry are enriched in the Gennargentu-region. 

First, we find that shared drift with Neolithic farmers and with pre-Neolithic hunter-gatherers is significantly correlated with the proportion of “Gennargentu-region” ancestral component estimated from ADMIXTURE analysis, while shared drift with Steppe pastoralists has a weak negative correlation with Gennargentu-region ancestry (Figure 6B). 

Second, using supervised estimation of ancestry proportion based on aDNA (Haak et al. 2015), we estimate higher levels of Neolithic and preNeolithic ancestries in the Gennargentu region and higher levels of Steppe Pastoralist ancestry outside the region (Figure S10). Finally, calculations with Patterson’s D-statistics of the form D(Outgroup, Ancient, Ogliastra, Non-Ogliastra) also support increased sharing with Neolithic and pre-Neolithic individuals, but not post-Neolithic individuals from the Steppe, in the Ogliastra samples (D = -0.0037 and -0.0042, |Z| = 7.4 and 7.9 when aDNA sample = Stuttgart and Loschbour, respectively; D = -0.0009, |Z| is not significant, when aDNA sample = Yamnaya) . 

Together, these results suggest that while at the regional-level Sardinia appears to harbor the highest amounts of Neolithic farmer ancestry and very little of the pre-Neolithic hunter-gatherer or Bronze Age pastoralists ancestries, there exists within-island variation. Specifically, we find that with increasing level of isolation (represented by increasing level of the Gennargentu ancestry), there are greater Neolithic farmer and pre-Neolithic hunter-gatherer ancestry, while the less isolated Sardinians have a stronger signal of ancestry from the Steppe pastoralist source. . . . 

We also found Sardinians show an impressive signal of shared ancestry with the Basque, in terms of identity-by-descent tracts and the outgroup f3 shared-drift metric. Such a connection is consistent with long-held arguments of a connection between the two populations, including claims of Basque-like non-Indo-European language words among Sardinian placenames (Blasco Ferrer 2010). More recently the Basque have been shown to be enriched for Neolithic farmer ancestry (Lazaridis et al. 2014, Gunther et al. 2015) and Indo-European languages have been associated with Steppe population expansions in the Bronze Age (Allentoft et al. 2015, Haak et al. 2015). These results support a model in which Sardinians and the Basque may both retain a legacy of pre-Indo-European, Neolithic ancestry (Gunther et al. 2015). . . . 

The high frequency of particular Y-chromosome haplogroups (particularly I2a1a2 and R1b1a2) that are not commonly affiliated with Neolithic ancestry is one challenge to a model in which Sardinian principally has Neolithic ancestry. Whether such haplogroup frequencies are due to simple genetic drift and/or a signal of sex-biased demographic processes has been an open question. By carrying out X versus autosome comparisons we uncovered evidence of sex-biased patterns of ancestry in Sardinia, and found an enrichment of Neolithic and preNeolithic ancestry on the X-chromosome across all groups on the island. 

The Abstract and Citation For The Paper

The population of the Mediterranean island of Sardinia has made important contributions to genome-wide association studies of traits and diseases. The history of the Sardinian population has also been the focus of much research, and in recent ancient DNA (aDNA) studies, Sardinia has provided unique insight into the peopling of Europe and the spread of agriculture. 

In this study, we analyze whole-genome sequences of 3,514 Sardinians to address hypotheses regarding the founding of Sardinia and its relation to the peopling of Europe, including examining fine-scale substructure, population size history, and signals of admixture. 

We find the population of the mountainous Gennargentu region shows elevated genetic isolation with higher levels of ancestry associated with mainland Neolithic farmers and depleted ancestry associated with more recent Bronze Age Steppe migrations on the mainland. Notably, the Gennargentu region also has elevated levels of pre-Neolithic hunter-gatherer ancestry and increased affinity to Basque populations. 

Further, allele sharing with pre-Neolithic and Neolithic mainland populations is larger on the X chromosome compared to the autosome, providing evidence for a sex-biased demographic history in Sardinia. These results give new insight to the demography of ancestral Sardinians and help further the understanding of sharing of disease risk alleles between Sardinia and mainland populations.

Charleston et al., Population history of the Sardinian people inferred from whole-genome sequencing, bioRxiv, Posted December 7, 2016, doi: http://dx.doi.org/10.1101/092148 via Eurogenes.

Druze Origins

The latest data on Druze origins is consistent with the leading existing data on the subject.

The Druze are an aggregate of communities in the Levant and Near East living almost exclusively in the mountains of Syria, Lebanon and Israel whose ~1000 year old religion formally opposes mixed marriages and conversions. Despite increasing interest in genetics of the population structure of the Druze, their population history remains unknown. 

We investigated the genetic relationships between Israeli Druze and both modern and ancient populations. We evaluated our findings in light of three hypotheses purporting to explain Druze history that posit Arabian, Persian or mixed Near Eastern-Levantine roots. 

The biogeographical analysis localised proto-Druze to the mountainous regions of southeastern Turkey, northern Iraq and southeast Syria and their descendants clustered along a trajectory between these two regions. The mixed Near Eastern–Middle Eastern localisation of the Druze, shown using both modern and ancient DNA data, is distinct from that of neighbouring Syrians, Palestinians and most of the Lebanese, who exhibit a high affinity to the Levant. Druze biogeographic affinity, migration patterns, time of emergence and genetic similarity to Near Eastern populations are highly suggestive of Armenian-Turkish ancestries for the proto-Druze.

Scarlett Marshall, et al., "Reconstructing Druze population history" Nature Scientific Reports 6, Article number: 35837 (November 16, 2016) (open access).

The paper also notes a modest level of admixture with local populations, particularly in Syria. In terms of the timing of this migration and ethnogenesis, a time period not long after Y1K seems likely in light of the historical and genetic evidence. The vicinity of Lake Van is particularly plausible as a core homeland of many pre-Druze people. None of the other populations of the Levant has the significant Turkish affinities of the Druze.

The conclusion to the paper notes that:

The biogeographical analysis localised many of the Druze to the Zagros Mountains and the mountains surrounding Lake Van and postulated that their migration path ran along a trajectory from southeast Turkey to southeast Syria. The dating analysis points to a major admixture event, which may have occurred towards the end of the Middle Ages in support of a Seljuk ancestry for the proto-Druze.

Interestingly, the paper hypothesizes that the Druze affinity for mountainous areas may reflect genetic adaptations to higher altitudes. The places where the Druze have the highest affinity seem to be largely Armenian and Kurdish.

The paper notes that Palestinians have a very localized origin, probably in continuity with the people of Israel who converted to Islam early in the Islamic expansion, and that the Lebanese show genetic affinity to Bedouins, probably during the late Roman Empire era and possibly in connection with Incense trade routes.

A notable observation about contemporary Druze culture is also found in the body of this open access paper:

In 2002, a survey of the Israeli Central Bureau of Statistics reported that the proportion of atheists among Israeli Druze is the highest of all Israelis (48%), including Jews (44%), Arabs (18%), Muslims (12%), and Christian Arabs (35%)41. 

An independent study examined the 145 officially recorded cases of Israeli Druze ‘straying’ from the religion, often motivated in part by a desire to marry outside the community39. Despite the excommunication fears, there has been a growing practice of exogamous marriages amongst Druze, particularly in the United States42 where inter-religious marriages, especially between Druze men and non-Druze women, are becoming more commonplace. These are becoming increasingly widespread in Israel43. However, such practices are expected to change according to the regional marriage laws that may be very strict. For example, in Lebanon, civil marriages are not allowed44, whereas in the US fewer prohibitions on marriage exist. With a lack of updated information regarding Druze marital practices, it is reasonable to conclude that the practice of exogamy is on the rise among the Druze, although it is difficult to assess whether this also entails a decline in the number of “religious” Druze due to the changing nature of this term. Secularisation processes, including the decline of strict religious practices such as endogamy5, especially among the younger generation40, can be expected to intensify the gene exchanges with neighbouring populations over time.

It is fascinating that two of the ethnic populations most formally defined by ancestral religion, the Druze and Jewish Israelis, are each almost half atheists, while "Christian" Arabs in Israel are more than a third atheists.

Another interesting contemporary observation about the populations of the region is that:

Levantine populations showed higher inbreeding coefficients and longer runs of homozygosity compared to Africans and Europeans, but lower compared to Central Asian and American populations. These results are to be expected given the high level of consanguinity among Druze (47%), Muslim Arabs (41.7%) and Bedouins (60.1%)57. The Druze’s effective population size (5,700 ± 300) is much higher than would be expected for a population isolate and is within the same order of magnitude as Palestinians (7,000 ± 300) and Bedouins (6,500 ± 300)58.

These levels of consanguinity are extremely high compared to most areas of Europe and North America, where the norm would be in the low single digit percentages, often below 2%.

Data Disfavors Self-Interacting Dark Matter Models

There are two leading dark matter particle theories: warm dark matter (involving particles of about 2 keV/c^2 mass that behave more or less like sterile neutrinos), and self-interacting dark matter (SIDM). A new paper concludes that one of those approaches, SIDM, is almost entirely ruled out by existing astronomy data.

Coupling dark matter to light new particles is an attractive way to combine thermal production with strong velocity-dependent self-interactions. Here we point out that in such models the dark matter annihilation rate is generically enhanced by the Sommerfeld effect, and we derive the resulting constraints from the Cosmic Microwave Background and other indirect detection probes. For the frequently studied case of s-wave annihilation these constraints exclude the entire parameter space where the self-interactions are large enough to address the small-scale problems of structure formation.

Torsten Bringmann, et al., "Strong constraints on self-interacting dark matter with light mediators" (December 2, 2016).

The conclusion of the paper notes that:

Models of DM with velocity-dependent self-interactions have recently received a great deal of attention for their potential to produce a number of interesting effects on astrophysical scales. We have shown in this Letter that these models face very strong constraints from the CMB and DM indirect detection. In the most natural realization of this scenario with a light vector mediator with kinetic mixing, these constraints rule out the entire parameter space where the self-scattering cross section can be relevant for astrophysical systems. These bounds remain highly relevant for a number of generalizations of the scenario, such as a different dark sector temperature and different mediator branching ratios. Clearly, future efforts to develop particle physics models for SIDM need to address these issues in order to arrive at models that provide a picture consistent with all observations in cosmology, astrophysics and particle physics.

So, at this point, dark matter particle theorists are pretty much stuck in a "warm dark matter or bust" position, as all alternatives are poorer fits to the data or are entirely contradicted by the data.

Then, scientists must determine if this one remaining decent contender in the dark matter particle arena can rival or outperform all of the several quite viable modified gravity theories that explain dark matter phenomena, some of which are particularly promising because they are inspired by quantum gravity corrections to general relativity.

Why Do Serbian And Sumerian Share Some Core Vocabulary?

At the Old European culture blog, some intriguing lexical connections between the Serbian language and words in the Sumerian language, that do not look like mere coincidences, have been identified. The Sumerian words are:

ISRUK = Gave (he gave) 

ISRUKAM = Gave (he gave to me)

NADANU = Give, Give (to pay)

The first two correspond to the proper phrase "iz ruku" which in a less formal speech register would be "iz rukama" (literally "from the hand" or "from the hands". Ruka is a root meaning "hand" or "arms" that is specific to the Slavic languages and borrowed from Slavic into the Balto-Slavic Lithuanian and Latvian languages.

The second corresponds to "Na dan" (masculine), "Na dana" (feminine), and "Na dano" (plural), with the word "Na" in this context representing a less formal speech register, meaning "give this to him". As the post author notes: "the Slavic verb "dati" meaning "to give" comes from Indoeuropean root "deh₃-", 

But the use of the word "Na" is idiosyncratic to Serbian. In the phase above it can mean "to" as part of a phrase, and in isolation as an imperative "Na!" it means "here you go", "here it is", or "take it".'

Why Is This Weird?

Languages borrow words all the time, what makes this unusual?

1. Completely Unrelated Language Families

The Sumerian language, spoken in Mesopotamia (i.e. modern day Iraq) is a language isolate that may be connected in some way to some other extinct non-Indo-European languages (such as Hurrian), but is in a completely different top level language family from the Indo-European language family that includes the Balto-Slavic languages that includes the Slavic languages that includes Serbian.

2. Lack of Overlap In Time

The Sumerian language was used in Mesopotamia at least as far back as 4000 BCE and was replaced in Mesopotamia by the Semitic Akkadian language (part of the Afro-Asiatic language family that is also completely unrelated to Indo-European languages) in everyday conversation around 2000 BCE. 

Sumerian lived own as a liturgical language, a bit like Latin in the Roman Catholic Church, Coptic in Ethiopian Orthodox religious use, Hebrew before it was resurrected for daily use in Israel, Classical Arabic in Islam (Arabic is a living language, but the Classical Arabic is about as remote from modern dialects as Middle English is from modern English), Sanskrit in Hindu religious contexts, Old Persian in Zoroastrian religious texts, and Hattic in Hittite Anatolia. But, Sumerian died as a liturgical language around the 1st century CE.

In contrast, Slavic wasn't spoken outside its homeland before the 5th century CE, and wasn't spoken in Serbia before the 6th century CE (five centuries after even liturgical use of Sumerian had ceased). Slavic is derived from a Balto-Slavic proto-language and from there from Proto-Indo-European. Proto-Indo-European, in turn, probably came into existence around 4000 B.C.E., but as recently as 2000 BCE, the Indo-European languages had only just reached South Asia, Iran, Greece, and the Tarim Basin, and there is a good argument that they had not reached Western Europe at all by that point.

For essentially all of the time period during which Sumerian was a living language, Indo-European languages were still predominantly found on the Pontic-Caspian Steppe where they originated, although they had begun to make inroads into Central Europe and the Baltic region.

3. Lack Of Immediate Geographic Proximity

Serbia is about 1,000 miles from Iraq roughly along the route taken by the first farmers to bring the Fertile Crescent Neolithic package to Europe.

This distance wouldn't be unprecedented for the expansion of a language family. But, there is no attested evidence of Sumerian or any language related to it, every making it further than the parts of Anatolia (modern Turkey), the Zagros Mountains (basically running along the modern Iraq-Iran border), and the southern Caucasus Mountains where the two highland areas intersect. Likewise, there is no evidence that Sumerian was ever spoken in the Levant or the Aegean.

The homeland of the Slavic languages is quite a bit further north in Poland and the Ukraine. 

Map showing 6th century Slavic territory and Slavic homeland from Wikipedia on "Slavs".

This homeland is also about 1,000 miles from Mesopotamia, but in this case, most easily by following the Tigris or Euphrates river to a source in the highlands of Anatolia and then descending to the Black Sea and following the Black Sea and Sea of Azov coast to the eastern most extent of this homeland.

The Slavic language only reached Serbia by the 6th century CE, at which point it was probably replacing now extinct Indo-European languages such as Latin and its likely predecessors in the area, Dacian and Thracian. 

Romanian, spoken in Romania which is between the Slavic homeland and Serbia, is a Romance language derived from Latin, but Serbian is not.

4. The Nature Of The Word Overlap

Languages that are not otherwise related routinely pick up loan words from each other. The Southeast Asian words for tea and many African fruits and vegetables which originated in Indonesia have often retained their original Asian names as loan words in the multitude of unrelated languages that purchased these trade goods.

The Mitanni people of the Northern Zagros Mountains in the Bronze Age ca. 1500 BCE, spoke a language very similar to Sanskrit (arguably a dialect of it, rather than a separate language). When the Hittites learned about horses from the Mitanni who were superior horsemen, they adopted the Mttanni technical terminology related to horses and abandoned the relevant words from their own vocabulary.

Sometimes loan words are also picked up because a language has a word or phrase that captures a meaning not found in the borrowing language, such as the adoption into English of the French phrase "je n'ai ce quio" (literally "I don't know what").

But, loan words are far less likely to replace every day vocabulary in a foreign language like "give", "give to me" or "pay". This core vocabulary tends to be much more resistant to fades and the effects of language contact.

5. The Apparent Direction Of The Word Overlap

Sumerian is an agglutinative language that takes what might be phrases or whole sentences in an isolating or analytical language like English into a single word. (Serbian, like many Indo-European languages is in the middle ground as a "fusional language" that is highly inflected, but does not strongly merge whole phrases into words.)

So, it is no surprise that in these cases of shared words, they are single words in Sumerian, but are a pair of words in Serbian.

But, the nature of the words in this case seem to reflect that the Sumerian words were borrowed from a predecessor to Serbian into Sumerian, instead of the other way around. 

The prepositional phrases in question in Serbian are combinations of words that have plain meaning as common words in isolation in Serbian. But, when broken apart, the components of the words in Sumerian have no independent meaning that implies the meaning of the whole.

Implications and Conclusions

How Did This End Up In Sumerian?

This suggests, in light of the other evidence, that the Serbian phrases "iz ruku", "iz rukama" and "na dano" must have existed in some very similar form either in actual Proto-Indo-European, or in a very early proto-language derived from it, and that somehow Sumerian ended up borrowing these core words into Sumerian.

The most likely place for this exchange of words would seem to be the Black Sea coast, the Caucasus Mountains, or Anatolia, which is in the middle ground between the Slavic homeland of the 5th century, and the furtherest extent of known Sumerian linguistic influence.

This is and of itself is pretty remarkable. While there is evidence of Sumerian borrowing of words from  the Hurrian language (discussed in a 2014 linguistic journal article[1] suggests is related either genetically or through heavy borrowing to the extinct Hurrian language of the northern highlands of the Zagros Mountains). I know of no other documented instances of Sumerian borrowing core vocabulary from an Indo-European language (Sumerian was no longer a living language, for example, by the time that the Indo-European Hittite language was widely spoken in neighboring Anatolia.)

I've also considered the possibility that the greater Hurrian language family extended as far as the Minoan language. And, it linguistic route of some phrases that have potential applications to trade interactions that were spoken in the Balkans by Indo-Europeans to the Minoans and from the Minoans to the Hurrians and from the Hurrians to the Sumerians, might be a plausible migration path for these words.

There is likewise, really no strong indication of cultural exchanges between Indo-Europeans and Sumerians, although Sumerian trade networks did bring it goods from places as distant as Afghanistan that could have included Indo-Europeans at distant ends of trade networks.

So, this language borrowing from some contemporary Indo-European language into Sumerian is still a real mystery, even with the wealth of clues available to us.

How Did This End Up In Serbian?

This also makes Serbian look particularly basal and conservative within the Indo-European languages relative to proto-Indo-European, despite the fact that as a distant branch of a sub-branch of a sub-branch of Indo-European, Serbian does not appear so basal in the overall structure of the Indo-European language family.

Could these words derive from a more basal Indo-European substrate of Serbian?

Given that both the unique meaning of the imperative "Na!" in Serbian meaning "I'm paying you" is specific to Serbian and the phrase "iz ruku" is specific to Slavic languages, it wouldn't be implausible to imagine that thees words are borrowed from the pre-Slavic, pre-Latin Indo-European languages spoken in the vicinity of Serbia prior to the expansion of the Roman era in the Bronze Age from ca. 2000 BCE to perhaps 600 BCE.

For example, an Indo-European substrate language to Serbian that would have had some influence at the time of language shift to the Slavic languages could have been an ill attested Indo-European language such as Dacian, or Thracian, or Illyrian, each of which are clearly much more basal branches of the Indo-European language family than Slavic, that could have persisted due to their character as core vocabulary in the area where they were substrate languages, across subsequent language shifts to Latin (probably limited to priests and other elites) and Slavic.

[1] Alexei Kassian, "Lexical Matches between Sumerian and Hurro-Urartian: Possible Historical Scenarios" (Cuniform Digital Library Journal Preprint October 3, 2014).

Malaria Was Common In The Roman Empire

[R]esearchers have discovered genomic evidence of malaria in 2,000-year-old human remains from the Roman Empire, according to a new study. 

With DNA fragments from the teeth of 58 adults and 10 children buried in three imperial-period Italian cemeteries, researchers were able to recover the mitochondrial genome to identify the specific malaria species that infected people. 

Their data confirm that it was the malaria parasite Plasmodium falciparum, the same one that is spread by mosquitoes today and kills hundreds of thousands of people every year. Symptoms include fever, chills and flu-like illness. 

"Malaria was likely a significant historical pathogen that caused widespread death in ancient Rome," said evolutionary geneticist and study author Hendrik Poinar, director of the Ancient DNA Center at McMaster University in Hamilton, Ontario. 

The researchers estimate that malaria killed as many people during the Roman Empire as it does now in Africa. In 2015, there were an estimated 438,000 malaria deaths worldwide, with 91% of them occurring in sub-Saharan Africa, according to the World Health Organization.

From here.

The headline of the media report above asks if malaria caused the fall of the Roman Empire, which is pretty much definitively a "no" because the samples taken are from three to four centuries before the empire fell.

It is notable that there is only a very thin historical record of this massive public health problem despite the depth of contemporaneous records we have from this area in this time period. The paper and abstract are as follows:

The historical record attests to the devastation malaria exacted on ancient civilizations, particularly the Roman Empire. However, evidence for the presence of malaria during the Imperial period in Italy (1st–5th century CE) is based on indirect sources, such as historical, epigraphic, or skeletal evidence. Although these sources are crucial for revealing the context of this disease, they cannot establish the causative species of Plasmodium. Importantly, definitive evidence for the presence of malaria is now possible through the implementation of ancient DNA technology. As malaria is presumed to have been at its zenith during the Imperial period, we selected first or second molars from 58 adults from three cemeteries from this time: Isola Sacra (associated with Portus Romae, 1st–3rd century CE), Velia (1st–2nd century CE), and Vagnari (1st–4th century CE). We performed hybridization capture using baits designed from the mitochondrial (mtDNA) genomes of Plasmodium spp. on a prioritized subset of 11 adults (informed by metagenomic sequencing). The mtDNA sequences generated provided compelling phylogenetic evidence for the presence of P. falciparum in two individuals. This is the first genomic data directly implicating P. falciparum in Imperial period southern Italy in adults.

Stephanie Marciniak, et al., "Plasmodium falciparum malaria in 1st–2nd century CE southern Italy" 26(23) Current Biology 1220-1222 (December 5, 2016).

Are Strange Quark Stars Possible? Maybe.

The prevailing assumption is that stable hadrons containing strange quarks are not possible. 

But, the Bodmer-Witten hypothesis is a conjecture that under the right conditions, stable matter containing strange quarks is possible. The hypothesis is named after papers by Bodmer and Witten respectively, making this conjecture, specifically: A. R. Bodmer, Phys. Rev. D 4 (1971) 1601. doi:10.1103/PhysRevD.4.1601 and E. Witten, Phys. Rev. D 30 (1984) 272.

But, a new paper examines the conditions under which a "strange quark star" could theoretically exist even in fairly sophisticated QCD models, and what its observable properties would be. Telescopes in the relatively near future should be able to determine if any observable stars have properties that would distinguish them as strange quark stars rather than ordinary stars, exist.

The abstract of the paper is vacuous, but the introduction to the paper explains that:

The so called Bodmer-Witten hypothesis on the absolute stability of strange quark matter still represents an open issue of nuclear and particle physics and its validity would have numerous important phenomenological implications in astrophysics (strange quark stars and strangelets in cosmic rays) and, possibly, also in cosmology (strangelets as a component of baryonic dark matter).

 

Verifying this hypothesis in terrestrial experiments is however very difficult because of the large net strangeness carried by this form of strongly interacting matter. 

On the other hand, theoretical calculations of the mass and density of strange quark matter droplets and of the thermodynamic properties of bulk strange quark matter are affected by large uncertainties due to the intrinsic difficulty of solving QCD at finite (but not asymptotically large) baryon densities.  

In this short contribution we will analyze two aspects related to the possibility of the existence of strange quark matter.  

First, we will show that this hypothesis can be fulfilled also in a class of quark models which feature not only confinement (as the MIT bag model) but also chiral symmetry. Specifically, we will show results obtained within the so-called chiral chromodielectric model.  

The second aspect concerns the astrophysical measurements of masses and radii of compact stars. Precise radii measurements (which will be feasible in the near future) could indeed unambiguously check the validity of the Bodmer-Witten hypothesis. Let us define R1.4 as the radius of a 1.4M⊙ compact star. As found in it is not possible to have a unique family of compact stars satisfying at the same time the condition R1.4 less than approximately 11km and Mmax ≤ 2M⊙. This conclusion has been confirmed also by other recent analyses. If future measurements will confirm the existence of stars for which R1.4 is less than approximately 11km, then one can conclude that strange quark stars co-exist with hadronic stars. In this two families scenario compact and light stars are hadronic stars whereas large and massive stars are strange quark stars. 

Since the ∼ 2M⊙ compact stars are, in this scenario, interpreted as strange quark stars that implies that the density of bound strange quark matter (i.e. the density corresponding to the minimum of the energy per baryon) is between 1-2 times nuclear matter saturation density. It is important to remark that although the absolute minimum of the energy per baryon of nuclear matter is located at a density similar to the density of strange quark matter they differ concerning the strangeness content. This implies that a direct transition from the metastable nucleonic state to the ground state of quark matter is suppressed because it requires multiple weak decays.

The conclusion then goes on to note that:

We have discussed the possibility of the existence of strange quark matter first within a purely theoretical approach, by using three different chiral models for quark matter and after within phenomenological approach through the measurements of masses and radii of compact stars.  

The Bodmer-Witten hypothesis could be fulfilled only if spontaneous chiral symmetry breaking and dynamical confinement are both implemented in the adopted quark model. In particular we have shown that a pure SU(3) quark meson chiral model, even in the presence of the additional dilaton field, does not allow for the existence of strange quark matter. Instead, in a simple confining chiral model, the chiral chromo-dielectric model, it is possible to find a window of parameters for which strange quark matter is absolutely stable.  

It is remarkable that the sets of parameters corresponding to these cases, are quite similar to the sets of parameters usually adopted for the study of hadronic observables.  

Finally, we have discussed what are the implications for the equation of state from the existence of massive compact stars and how future measurements of radii can be used to test fundamental properties of dense matter.  

In particular, a strong indication of the validity of the Bodmer-Witten hypothesis will be measurements of R1.4 less than approximately 11 km. The existence of stars as massive as 2M⊙ (or more) would indicate that if the Bodmer-Witten hypothesis is correct, the (second) minimum of the energy per baryon of strongly interacting matter is located at a density slightly above the nuclear matter saturation density. Differently from the minimum corresponding to nuclear matter, this second minimum would contain a net strangeness fraction close to 1/3. The possibility to search for this kind of matter also in terrestrial experiments would be in this case very promising.

Astronomy observations that could distinguish between strange quark stars and more ordinary massive small stars will soon be available to test this possibility.

 

Progress Made In Measuring Bottom Quark Yukawa Coupling

In the Standard Model, the rest mass of the bottom quark at various energy scales arises from its Yukawa coupling to the Higgs boson, but this is hard to measure with precision directly. Direct measurements have a precision of only about +/- 20%.

There are other ways to more precisely measure quantities related in principle to the bottom quark Yukawa coupling. But, it has been challenging to convert the measured quantities to the theoretically fundamental Yukawa coupling in a precise and rigorous way.

A new paper has refined the formula for converting the more easily measured mass quantities to the more fundamental Yukawa coupling value associated with it. It does so by making a calculation out to more loops than is customary, by including QED corrections which are important, while omitting corrections that are difficult to calculate but are demonstrated in the paper to be immaterial in magnitude relative to other sources of error, in this particular calculation.

The increased precision in the indirectly measured experimentally determined value of the bottom quark Yukawa coupling to the Higgs boson is particularly helpful in refining Standard Model predictions for the rate at which a Standard Model Higgs boson should decay to bottom-antibottom quark pairs (the most common mode of Higgs boson decay, although not the easiest to measure due to background processes that inject noise into the Higgs boson decay signal).

Reducing the Standard Model theoretical prediction error to a minimum increases the power of any given experimental test of the accuracy of that prediction somewhat.

Another Experimental Confirmation of Lepton Universality

Yet another experimental result has quashed early hints of potential beyond the Standard Model physics.

A new study of the decays of anti-B mesons to D* mesons and leptons at Belle, confirms the Standard Model prediction of lepton universality (i.e. that tau leptons, muons and electrons have weak force decays that are identical to each other except to the extent that their different masses factor into the process and then only to the extent justified by their differing masses).

Some previous experimental results for this measurement were in tension with the Standard Model prediction for this measurement, providing one of the more notable currently outstanding experimental discrepancies with the Standard Model's predictions, first widely noted in early 2015.

Previous experiments casting doubt on lepton universality violations involved different kinds of decays than those in which the tensions with the Standard Model had been noted. A 2015 paper from LHCb involving tau decays, and a 2015 paper involving pion decays at the LHC have similarly found no violation of lepton universality. Neither did a 2014 paper looking at Z boson decays. But, this paper was the first to strongly refute evidence a lepton flavor universality violation in the same decays where they had been previously hinted at by the experimental evidence. As the paper explains:

Semileptonic B decays to τ leptons (semitauonic decays) are sensitive to new physics (NP) beyond the Standard Model (SM), such as an extended Higgs sector. A prominent candidate is the Two-Higgs-Doublet Model . . . for the decay process B¯ → D(∗) τ −ν¯τ. The decays B¯ → D(∗) τ −ν¯τ have been studied by the Belle, BaBar and LHCb experiments. Most of these studies have measured ratios of branching fractions, defined as R(D(∗) ) = B(B¯ → D(∗) τ −ν¯τ )/B(B¯ → D(∗) l−ν¯l−). The denominator is the average of l− = e−, µ− for Belle and BaBar, and l− = µ− for LHCb. The ratio cancels numerous uncertainties common to the numerator and the denominator.  

The current averages of the three experiments are R(D) = 0.397 ± 0.040 ± 0.028 and R(D∗ ) = 0.316 ± 0.016 ± 0.010, which are 1.9 and 3.3 standard deviations (σ) away from the SM predictions of R(D) = 0.299 ± 0.011 or 0.300 ± 0.008 and R(D∗ ) = 0.252±0.003, respectively. The overall discrepancy with the SM is about 4σ. These tensions have been studied in the context of various NP models. . . .

Our study includes an R(D∗) measurement independent of the previous studies, in which leptonic τ decays have been used. 

This study examined the relevant decay from 772,000,000 B-anti-B meson pair decays. Based upon this data if finds that:

Our results . . . R(D∗) = 0.270 ± 0.035(stat.) +0.028 −0.025(syst.), are consistent with the theoretical predictions of the Standard Model.

In particular, the results are consistent with the Standard Model at the 1 sigma level, greatly reducing the overall tension in the experimental data from all of the experiments combined.

The study also for the first time examined the polarization of the tau leptons produced in these decays, which is sensitive to the same kinds of beyond the Standard Model physics that would lead to lepton non-universality, and found that the polarizations were also consistent with the Standard Model prediction. 

The SM predicts Pτ (D) = 0.325 ± 0.009 and Pτ (D∗ ) = −0.497 ± 0.013. . . . In this Letter, we report the first Pτ (D∗ ) measurement in the decay B¯ → D∗ τ −ν¯τ with the τ decays τ − → π −ντ and τ − → ρ −ντ . 

Belle's experimental result, Pτ (D ∗ ) = −0.38±0.51(stat.) +0.21 −0.16 (syst.), is also consistent with the Standard Model prediction, although this is somewhat less notable because the experimental measurement isn't very precise.

So, tensions in the previous studies by the Belle, BaBar and LHCb experiments with the Standard Model predictions are increasingly looking like statistical flukes.

200 Ancient Bell Beaker Genomes To Be Released March 2017

One of the biggest mysteries in the study of the historical linguistics and population genetics of Europe is the role played by the Bell Beaker culture. 

One view sees it as a small number of culturally influential traders, craftsmen and priests. Another sees it as a major folk migration. Its putative origins range from North Africa to Iberia to Germany to the Balkans to the Baltics to Crete to the European Steppe. Some see it as a linguistically Indo-European source for the Celtic languages. Others see it as linguistically Vasconic, a language family now represented by only one living language, Basque.

This spring, according to Jean Marco via Eurogenes we are going to have a lot more clues to work from:

Reporting back on the lecture on Bell Beaker by Volker Heyd this evening in Dorchester. The expected two aDNA papers on Bell Beaker have been delayed for the best possible reason. The two teams, one from Harvard and the other from Copenhagen, have agreed to amalgamate their results into one huge paper, which will give the results of over 200 samples. It is due to be published in a couple of months. Until then all the results are embargoed. Volker Heyd would only say that they are exciting. 

He would also prefer me not to divulge everything he said at the lecture on the archaeological side, since he has a paper coming out in the March issue of Antiquity on Bell Beaker; while in the same issue will be one by Kristiansen on Corded Ware. So I'll be brief. He went through the various theories of the origins of Bell Beaker: the Dutch model prevalent until the 1990s, the change wrought by the Muller and Van Willigen radiocarbon date compilation of 2001 and subsequent publications of early dates in Iberia, the various attempts to make sense of an Iberian origin. The problem of the latter and of the idea of a North African origin are the same in his view. There is no prior usage of cord in pottery decoration of either. So he sticks by the Yamnaya link to a pre-BB culture proposed in Harrison and Heyd 2007. The icing on the cake lies in two significant new discoveries, which are not entirely published as yet.

The referenced paper and its abstract are as follows:

The megalithic cemetery of Sion-'Le Petit Chasseur I+III' offers a unique chance to analyse patterns of social change throughout most of the third millennium BC, and to demonstrate how a local population adjusts to the pan-European ideological changes of that period. Our analysis of the funeral monuments, the anthropomorphic stelae, and the material remains (which form three independent Quellengruppen) shows the tensions between tradition and innovation, and the successive adaptions of a local Late Neolithic population to the different branches of the Bell Beaker ideology and the Early Bronze Age. We compare Sion with the similar structured site of Aosta-'St.Martin-de-Corléans', and locate both complexes in the wider framework of Europe in the third millennium BC. The comparison extends to include the immigration of the Yamnaya populations from the northern Pontic steppes into east and southeast Europe, and ends with the emergence of the Bell Beaker phenomenon on the west of the Iberian Peninsula. This is all set into the wider transformation horizon between 2900 and 2700 BC. Specific innovations are described and analysed.

Richard Harrison and Volker Heyd, "The Transformation of Europe in the Third Millenium BC: the example of 'Le Petit-Chasseur I +III' (Sion, Valais, Switzerland)", 82(2) Praehistorische Zeilschrift 129-214 (January 2007).

Bell Beaker Blogger has more good analysis of this news. Some of his key insights:

This March paper in Cambridge's Antiquity will be a revisit of an important paper that appeared in Antiquity in 1974, "Origins of the Bell Beaker cultures" by Richard J. Harrison. Harrison proposed a model for the formation of the Bell Beaker culture . . . . 

To sum it up rather succinctly, Afro-Iberian Maritime Beakers electrocuted themselves in the domain of the Single Grave Culture of the Dutch Rhine. When the door of the tele-transport opens, a sort of hybrid steps out and then clobbers Europe and North Africa from this location. . . .

Another paper will be penned by Kristain Kristainsen, probably concerning the origins of the Dutch Single Grave Culture. I'll assume that we will see a fluctuation in Steppe Ancestry from the beginning of the SGC where it spikes, and then its diminishing as the Bell Beaker culture begins to take hold. 

So now I'll speculate on what surprises may be in store that would truly be surprising. Surprising would be if they were able to isolate the two components at the earliest phase, like a PFB that was R1b-M269 and a MN-styled Maritime Iberian in the Lower Rhine at about the same time (or some weird combination). 

Overall, I think that despite the far-flung regions where they may have genomes, they might be looking hard at a fusion area in the vicinity of the Lower Rhine.

One Of The Most Amazing Things About Los Angeles Is Completely Natural

When you start cataloguing the natural wonders of the world, Los Angeles, California, which is known for its artifice, glitz and traffic jams, probably isn't what comes first to mind. 

But, Los Angeles is home to the La Brea Tar Pits which have produced: "Hundreds of thousands of fossils of Late Pleistocene animals and plants have been recovered at this one site." It is the most productive fossil dig in the world and has produced bones of animals (many extinct) that range from 50,000 years old to a few centuries old. An astonishing 70% are carnivores because "an herbivore ended up trapped in the sticky tar, and was feasted upon by carnivores, which then themselves ended up getting stuck too."

Twilight Beasts has an excellent profile piece on the site.

Academics Aren't Paid (Directly) For Their Publications

As 4Gravitons (who is a graduate student or post-grad at the Perimeter Institute in Waterloo, Canada, one of the premier theoretical physics shops in the world) recently pointed out in his blog:

In fact, academics don’t get paid by databases, journals, or anyone else that publishes or hosts our work. In the case of journals, we’re often the ones who pay publication fees. Those who write textbooks get royalties, but that’s about it on that front.

I grew up with a father who was a professor and a mother who was a university administrator who helped professors get grants for research and comply with human subjects requirements, so I've know this for as long as I knew it was something to know about. But, lots of people don't realize this fact.

Now, this doesn't mean that professors don't receive economic benefit from publishing. The business model of academia works like this:

1. You need to do research, ideally publishable in some form, to earn a PhD, and a PhD or good progress towards earning one in the very near future, is the basic prerequisite for being hired as a professor.

2.  Professors are initially hired for one to three year fixed terms as lecturers or as tenure track "Assistant Professors".

3.  An Assistant Professor is evaluated for tenure (usually after three years, but practice varies and sometimes there are multiple stints as an Assistant Professor at the same institution or successive ones). If you get tenure, you are usually simultaneously promoted to "Associate Professor" and get a raise. If you don't get tenure, you may be given another shot, but usually, you are terminated.

4.  An Associate Professor with tenure can then be evaluated for promotion to full "Professor" with greater prestige and higher pay.

In all of the main career steps in an academic's life: getting a PhD, getting hired as a tenure track professor, earning tenure, getting promoted to Associate Professor, and getting promoted to full Professor, the dominant consideration is what research you have published in peer reviewed scholarly journals and how significant that research is (e.g. measured by citations in other scholarly work). There are other factors, but that is the dominant one. Hence the phrase, "publish or perish".

Your publications are also the primary consideration in how prestigious and high paying a post you will be hired at (often after landing a first post elsewhere) and of your prestige in your field and the academic profession in general.

A professor at a research university has a teaching load expected to use about 25%-67% of his or her time, with the most esteemed professors having the lightest teaching loads. In the balance of your time you are expected, but not required (once you have tenure) to do research, most of which should be potentially publishable in peer reviewed journals.

Subsidies for universities and colleges from state governments that make this possible is the main way that state government finances basic research.

So professors have strong incentives to publish, but are not directly rewarded for the publications themselves (many of which have arguably weak claims to intellectual property protection due to exceptions for factual compilations and scientific principles).

This is a good thing, because, in the end, their incentive is to produce more papers, not necessarily for those papers to have lots of readers, and even very respectably cited papers are often read by a very small number of readers and purchased by few customers other than academic libraries.

Emergent Gravity

Sabine Hossenfelder's latest post at Backreaction on "Emergent Gravity" is one of her best educated layman oriented posts explaining concepts in fundamental physics yet.

Notably, she emphasizes the connection, lacking in many other explanations of this approach, to the similarities between thermodynamics (which is know is emergent via statistical mechanics from the mechanics of atoms and molecules) and gravity.

Emergent gravity has been in the news lately because of a new paper by Erik Verlinde. 

. . . 

Almost all such attempts to have gravity emerge from some underlying “stuff” run into trouble because the “stuff” defines a preferred frame which shouldn’t exist in general relativity. They violate Lorentz-invariance, which we know observationally is fulfilled to very high precision. 

An exception to this is entropic gravity, an idea pioneered by Ted Jacobson 20 years ago. Jacobson pointed out that there are very close relations between gravity and thermodynamics, and this research direction has since gained a lot of momentum. 

The relation between general relativity and thermodynamics in itself doesn’t make gravity emergent, it’s merely a reformulation of gravity. But thermodynamics itself is an emergent theory – it describes the behavior of very large numbers of some kind of small things. Hence, that gravity looks a lot like thermodynamics makes one think that maybe it’s emergent from the interaction of a lot of small things. . . . as long as you’re not looking at very short distances, it might not matter much exactly what gravity emerges from. Like thermodynamics was developed before it could be derived from statistical mechanics, we might be able to develop emergent gravity before we know what to derive it from.

This is only interesting, however, if the gravity that “emerges” is only approximately identical to general relativity, and differs from it in specific ways. For example, if gravity is emergent, then the cosmological constant and/or dark matter might emerge with it, whereas in our current formulation, these have to be added as sources for general relativity. 

So, in summary “emergent gravity” is a rather vague umbrella term that encompasses a large number of models in which gravity isn’t a fundamental interaction. The specific theory of emergent gravity which has recently made headlines is better known as “entropic gravity” and is, I would say, the currently most promising candidate for emergent gravity. It’s believed to be related to, or maybe even be part of string theory, but if there are such links they aren’t presently well understood.

She references the following article for a more technical description of many of the leading theories.

We give a critical overview of various attempts to describe gravity as an emergent phenomenon, starting from examples of condensed matter physics, to arrive to more sophisticated pregeometric models. The common line of thought is to view the graviton as a composite particle/collective mode. However, we will describe many different ways in which this idea is realized in practice.

Lorenzo Sindoni, Emergent Models for Gravity: an Overview of Microscopic Models (May 12, 2012).

The notion that you might be able to derive gravity from first principles through a clever macro-level understanding of particle physics is very exciting indeed. It would be miraculous enough for dark matter and dark energy to emerge naturally from a quantum gravity theory. But, it would be even more amazing if quantum gravity itself could be derived from and emerged naturally from fundamental particle physics. 

Certainly, that hasn't been established yet, but it does seem like a very plausible possibility.

Glueballs Still Elusive

Despite combing through 260 million events that should be able to produce a type of glueball resonance that can't be confused with quarkonium, the researchers once again after about four decades of fruitless searching, have come up empty. The quality of this particular search at Belle, and the relentless failure of searches over the decades to find any trace of glueballs despite increasingly sophisticated efforts to find them has me wondering: 

Does some, as yet unarticulated missing principle of quantum chromodynamics (QCD) forbids glueballs?

The particularly confounding aspect of this is that glueballs are relatively easy to describe mathematically, since they implicate just one of the Standard Model physical constants, the strong force coupling constant. Unlike other hadrons, no physical constants related to quark masses, the weak force coupling constant, or the CKM matrix needs to be known to describe them. 

The masses they are predicted to have are not very different from all sorts of other known hadrons (this search focused on glueballs predicted to have masses from 2.8 to 4.59 GeV (at two sigma extremes from the predicted masses), around the predicted mass of D mesons and B mesons, and well defined, distinctive quantum numbers. These are essentially completely defined from theory.

A search with 260 million events shouldn't be able to miss them if they are produced at all in the studied process at any meaningful rate, but the collaborators found nothing. Branching fractions of as much as 1 per 5,000 decays to glueballs from the Upsilon mesons whose decays were studied, which were promising candidates for giving rise to decay to glueballs at a detectable branching fraction, have been ruled out.

What do we not know about QCD that causes this? If they do exist, why can't we find traces of any of them?

The fact that these are "oddballs" can mix with quarkonium states is particularly notable, because the usual excuse for not being able to see glueball resonances doesn't apply here.

In QCD, the usual rule is that everything that is permitted is mandatory, so finding a decay that isn't prohibited by any of the rules of QCD that can't be detected is a big signal that we're missing something, although it is notable that no QCD theoretical estimate of the branching fraction was provided in this study, as some resonances are simply very rare.

The existence of bound states of gluons (so-called “glueballs”), with a rich spectroscopy and a complex phenomenology, is one of the early predictions of the non-abelian nature of strong interactions described by quantum chromodynamics (QCD). However, despite many years of experimental efforts, none of these gluonic states have been established unambiguously. Possible reasons for this include the mixing between glueballs and conventional mesons, the lack of solid information on the glueball production mechanism, and the lack of knowledge about glueball decay properties. Of these difficulties, from the experimental point of view, the most outstanding obstacle is the isolation of glueballs from various quarkonium states.

Fortunately, there is a class of glueballs with three gluons and quantum numbers incompatible with quark-antiquark bound states, called oddballs, that are free of this conundrum. The quantum numbers of such glueballs include J P C = 0 −−, 0 +−, 1 −+, 2 +−, 3 −+, and so on. Among oddballs, special attention should be paid to the 0 −− state (G0−− ), since it is relatively light and can be produced in the decays of vector quarkonium or quarkoniumlike states.

Two 0 −− oddballs are predicted using QCD sum rules with masses of (3.81 ± 0.12) GeV/c 2 and (4.33 ± 0.13) GeV/c 2 , while the lowest-lying state calculated using distinct bottom-up holographic models of QCD [3] has a mass of 2.80 GeV/c 2 . Although the masses have been calculated, the width and hadronic couplings to any final states remain unknown.

Possible G0−− production modes from bottomonium decays are suggested in Ref. [2] including Υ(1S, 2S) → χc1+G0−− , Υ(1S, 2S) → f1(1285)+G0−−, χb1 → J/ψ+G0−− , and χb1 → ω + G0−− . In this paper, we search for 0 −− glueballs in the production modes proposed above and define G(2800), G(3810), and G(4330) as the glueballs with masses fixed at 2.800, 3.810, and 4.330 GeV/c 2 , respectively. All the parent particles in the above processes are copiously produced in the Belle experiment, and may decay to the oddballs with modest rates.

Full pdf here.

The abstract and paper are as follows:

We report the first search for the J P C = 0−− glueball in Υ(1S) and Υ(2S) decays with data samples of (102 ± 2) million and (158 ± 4) million events, respectively, collected with the Belle detector. No significant signals are observed in any of the proposed production modes, and the 90% credibility level upper limits on their branching fractions in Υ(1S) and Υ(2S) decays are obtained. The inclusive branching fractions of the Υ(1S) and Υ(2S) decays into final states with a χc1 are measured to be B(Υ(1S) → χc1 + anything) = (1.90 ± 0.43(stat.) ± 0.14(syst.)) × 10⁻⁴ with an improved precision over prior measurements and B(Υ(2S) → χc1 + anything) = (2.24 ± 0.44(stat.) ± 0.20(syst.)) × 10⁻⁴ for the first time.

Belle Collaboration, "Search for the 0−− Glueball in Υ(1S) and Υ(2S) decays" (November 22, 2016).

UPDATE November 29, 2016:

A preprint of a back to the drawing board paper has been posted and notes these results while estimating a best fit for an oddball mass two GeV heavier than the mass used by the Belle Collaboration that is still consistent to within the large two sigma error bars with the heavier Belle Collaboration values.

We present the new results for the exotic glueball state 0−− in the framework of the QCD sum rules. It is shown that previously used three-gluon current does not couple to any glueball bound state. We suggest considering a new current which couples to this exotic state. The resulting values for mass and decay constant of the 0−− glueball state are MG = 6.3 +0.8 −1.1 GeV and FG = 67 ± 6 keV, respectively.

Alexandr Pimikov, Hee-Jung Lee, Nikolai Kochelev, Pengming Zhang, "Revision of exotic 0−− glueball" (November 26, 2016).

Their predicted mass at two sigma error bars is 4.1 GeV to 7.9 GeV which isn't too impressive for a pure theoretical calculation that is basically a function of just one experimentally measured Standard Model constant (the strong force coupling constant) that is known to a precision of about 1%. The Belle estimate has a mere 3% uncertainty.

The pseudo-scalar bottom eta meson which is a form of bottomonium has a mass of 9.398 +/- 0.0032 GeV. The measured mass of the parent mesons Y(1S) which is called an upsilon meson, is also a form of bottomonium and is 9.46030 +/- 0.00026 GeV. The measured mass of the Y(2S) which is an excited upsilon meson, which is another form of bottomonium isn't well established in sources I've found off the bat, but would be expected to be heavier than 9 .46 GeV. Measured masses of two kinds of Y bosons with the right quantum numbers whose exact excitation has not been determined are 10.81 GeV and 11.02 GeV. So, the parent would not be barred from decaying into an oddball of this type even if it is on the heavy side of the estimated range, by mass-energy conservation.

The introduction to this paper notes that:

The glueballs are composite particles that contain gluons and no valence quarks. The glueballs carry very important information about the gluonic sector of QCD and their study is one of the fundamental tasks for the strong interaction. While the glueballs are expected to exist in QCD theoretically, there was no clear experimental evidence and so the glueballs remain yet undiscovered (see reviews [1, 2]). This is the reason why the investigation of the possible glueball’s candidates are included in the programs of the running and projected experiments such as Belle (Japan), BaBar (SCAC, USA), BESIII (Beijing, China), RHIC (Brookhaven, USA), LHC (CERN), GlueX (JLAB, USA), NICA (Dubna, Russia), HIAF (China) and FAIR (GSI, Germany). 

One of the main problems of the glueball spectroscopy is the possible large mixing of the glueballs with ordinary meson states, which leads to the difficulties in disentangling the glueballs in the experiment. In this connection, the discovery of the exotic 0−− glueball, which can not be mixed with the qq¯ states, is one of the fundamental tasks of the glueball spectroscopy. Therefore, it is very important to investigate the properties of this glueball within the QCD’s based approach. One of such approaches is the QCD Sum Rules (SR). The first study of the 0−− glueball by the QCD SR method has been performed recently in [3] where the authors introduced a very specific interpolating current for this three-gluon state. Unfortunately, they only considered SR for the mass of the glueball and did not check the SR for the decay constant. Below we show that their current has pathology, which leads to the negative sign of the imaginary part of the corresponding correlator and, as the result, SR become inconsistent. Considering the fact the study of the glueball is a very hot topic nowadays and the prediction of the value of the exotic glueball mass is crucial for the experimental observation, the revision of the exotic glueball properties within QCD SR is required. 

In this Letter, a new interpolating current, which couples to the 0−− exotic glueball state, is suggested. We calculate the Operator Product Expansion (OPE) for the correlator with this current up to dimension-8 and show that there is a good stability of SR for both mass and decay constant of this state.

The paper then reaches the result stated in the abstract and goes on to conclude that:

Our final result is: MG = 6.3 +0.8 −1.1 GeV,  FG = 67 ± 6 keV. (11)

The SR analysis in full QCD (Nf = 3) and nonzero quark condensate hJ 2 i) leads to a reduction of the glueball mass by 0.2 GeV. The mass of the exotic glueball in Eq.(11) is not far away from the recent unquenched lattice result MG = 5.166 ± 1.0 GeV [12] obtained with a rather large pion mass mπ = 360 MeV. 

Here we would like to note that there are three sources of uncertainties in the above analysis for the mass and decay constant: the variation of gluon condensate, stability of SR triggering Borel parameter M2 dependence in terms of criteria δ min k , and roughly estimated SR uncertainty coming from the OPE truncation. The latter uncertainty for the decay constant comes from the definition of the fiducial interval, Eq. (9), in the standard assumption that the contribution from missing terms is of the order of the last included nonperturbative term squared: (1/3)2 ∼ 10%. The same error for mass can be expected to be suppressed since the related errors for R (SR) k+1 and R (SR) k are correlated. The best threshold value is s bf 0 = 52.4 +12.6% −16.2% GeV2 when only uncertainty of the gluon condensate is included. Note that the fiducial interval for the central value of the gluon condensate is M2 ∈ [3.7, 7.3] GeV2 . We also mention that here we present the results from the k = 0 case for SR (see Eqs.(8,10)). The mass estimation for higher values of k = 1, 2, 3 are in agreement with the considered k = 0 case within the error bars. 

Summarizing, we present the revision of the QCD SR result for the exotic three-gluon glueball state with quantum numbers J P C = 0−−. A new interpolating current for this glueball has been constructed. By using this current, we have analyzed the QCD SR consisting of contributions up to the operators of dimension-8 and obtained the estimation of the mass and decay constant of the exotic glueball. 

After the paper was completed we were informed about the negative result of the searching of the low mass exotic 0 −− glueball by the Belle Collaboration.

UPDATE (December 4, 2016): Marco Frasca has some interesting comments on the subject here.

Turkey History

Like pumpkins, squash and gourds, Turkeys were domesticated in the Americas in the pre-Columbian era, possibly near Oaxaca, Mexico, where I went on my honeymoon (a long, long time ago).

The turkeys we'll be sitting down to eat on Thursday have a history that goes way back. Archaeologists have unearthed a clutch of domesticated turkey eggs used as a ritual offering 1,500 years ago in Oaxaca, Mexico -- some of the earliest evidence of turkey domestication. . . .

"The fact that we see a full clutch of unhatched turkey eggs, along with other juvenile and adult turkey bones nearby, tells us that these birds were domesticated," says Feinman. "It helps to confirm historical information about the use of turkeys in the area." 

The eggs, according to Feinman, were an offering of ritual significance to the Zapotec people. The Zapotec people still live in Oaxaca today, and domesticated turkeys remain important to them. "Turkeys are raised to eat, given as gifts, and used in rituals," says Feinman. "The turkeys are used in the preparation of food for birthdays, baptisms, weddings, and religious festivals." 

The new information about when turkeys were domesticated helps amplify the bigger picture of animal domestication in Mesoamerica. "There were very few domesticated animals in Oaxaca and Mesoamerica in general compared with Eurasia," explains Feinman. "Eurasia had lots of different meat sources, but in Oaxaca 1,500 years ago, the only assuredly domestic meat sources were turkeys and dogs. And while people in Oaxaca today rely largely on meat from animals brought over by the Spanish (like chicken, beef, and pork), turkeys have much greater antiquity in the region and still have great ritual as well as economic significance today." 

The turkeys that are so important to the Zapotec today are similar birds to the ones that play a role in the American tradition of Thanksgiving. "These are not unlike the kinds of turkeys that would have been around at the first Thanksgiving, and similar to the birds that we eat today," says Feinman.

From here. Based upon the following journal article:

Highlights

• Mitla Fortress yields clear evidence for turkey domestication in southern Mexico. 

• Domesticated turkeys were present in the Valley of Oaxaca by the mid Classic period (ca. CE 400–600). 

• Turkeys were raised for subsistence, ritual offerings, and marketable goods. 

• Remains include juvenile and adult birds (hens and toms), whole eggs, and numerous eggshell fragments at least one egg-laying hen present. 

• SEM images of the eggshell reveals both unhatched and hatched eggs from a range of incubation stages. 

Abstract 

Recent excavations of two domestic residences at the Mitla Fortress, dating to the Classic to Early Postclassic period (ca. CE 300–1200), have uncovered the remains of juvenile and adult turkeys (both hens and toms), several whole eggs, and numerous eggshell fragments in domestic refuse and ritual offering contexts. Holistically, this is the clearest and most comprehensive evidence to date for turkey domestication in the Central Valleys of Oaxaca, Mexico. Juvenile turkeys range in age, from recently hatched poults to young juvenile birds. Medullary bone, which only forms in female birds before and during the egg-laying cycle, indicates the presence of at least one egg-laying hen. Scanning electron microscope (SEM) images of the eggshell reveals both unhatched and hatched eggs from a range of incubation stages, from unfertilized or newly fertilized eggs to eggs nearing the termination of embryogenesis to hatched poults. We present these new data and explore turkey husbandry, consumption, and use by two residential households at the Mitla Fortress.

Heather A. Lapham, Gary M. Feinman, Linda M. Nicholas. "Turkey husbandry and use in Oaxaca, Mexico: A contextual study of turkey remains and SEM analysis of eggshell from the Mitla Fortress." Journal of Archaeological Science: Reports (July 1, 2016)

Pumpkin History

Happy Thanksgiving (with a hat tip to CNN)!

Pre-Columbian hunters and gatherers may have proto-farmed pumpkins, squash and gourds, which were domesticated in the Americas, after their survival was threatened by the megafauna extinction caused by their arrival in the Americas. 

Significance 

Squashes, pumpkins, and gourds belonging to the genus Cucurbita were domesticated on several occasions throughout the Americas, beginning around 10,000 years ago. The wild forms of these species are unpalatably bitter to humans and other extant mammals, but their seeds are present in mastodon dung deposits, demonstrating that they may have been dispersed by large-bodied herbivores undeterred by their bitterness. However, Cucurbita may have been poorly adapted to a landscape lacking these large dispersal partners. Our study proposes a link between the disappearance of megafaunal mammals from the landscape, the decline of wild Cucurbita populations, and, ultimately, the evolution of domesticated Cucurbita alongside human cultivators. 

Abstract 

The genus Cucurbita (squashes, pumpkins, gourds) contains numerous domesticated lineages with ancient New World origins. It was broadly distributed in the past but has declined to the point that several of the crops’ progenitor species are scarce or unknown in the wild. We hypothesize that Holocene ecological shifts and megafaunal extinctions severely impacted wild Cucurbita, whereas their domestic counterparts adapted to changing conditions via symbiosis with human cultivators. 

First, we used high-throughput sequencing to analyze complete plastid genomes of 91 total Cucurbita samples, comprising ancient (n = 19), modern wild (n= 30), and modern domestic (n = 42) taxa. This analysis demonstrates independent domestication in eastern North America, evidence of a previously unknown pathway to domestication in northeastern Mexico, and broad archaeological distributions of taxa currently unknown in the wild. Further, sequence similarity between distant wild populations suggests recent fragmentation. Collectively, these results point to wild-type declines coinciding with widespread domestication. 

Second, we hypothesize that the disappearance of large herbivores struck a critical ecological blow against wild Cucurbita, and we take initial steps to consider this hypothesis through cross-mammal analyses of bitter taste receptor gene repertoires. Directly, megafauna consumed Cucurbita fruits and dispersed their seeds; wild Cucurbita were likely left without mutualistic dispersal partners in the Holocene because they are unpalatable to smaller surviving mammals with more bitter taste receptor genes. Indirectly, megafauna maintained mosaic-like landscapes ideal for Cucurbita, and vegetative changes following the megafaunal extinctions likely crowded out their disturbed-ground niche. Thus, anthropogenic landscapes provided favorable growth habitats and willing dispersal partners in the wake of ecological upheaval.

Logan Kistler, et al., "Gourds and squashes (Cucurbita spp.) adapted to megafaunal extinction and ecological anachronism through domestication" 112 P.N.A.S. 15107-15112 (December 8, 2015).

Pumpkins, squashes and gourds were domesticated by pre-Columbian Native Americans many thousands of years ago from five different wild species, three of which still exist today and two of which have no known wild ancestors that still exist. Genetic evidence shows no evidence of crossing of subspecies of Cucurbita. The family tree of these plant sub-species is as follows:

Genetic relationships among 104 accessions of Cucurbita pepo were assessed from polymorphisms in 134 SSR (microsatellite) and four SCAR loci, yielding a total of 418 alleles, distributed among all 20 linkage groups. Genetic distance values were calculated, a dendrogram constructed, and principal coordinate analyses conducted. The results showed 100 of the accessions as distributed among three clusters representing each of the recognized subspecies, pepo, texana, and fraterna. The remaining four accessions, all having very small, round, striped fruits, assumed central positions between the two cultivated subspecies, pepo and texana, suggesting that they are relicts of undescribed wild ancestors of the two domesticated subspecies. In both, subsp. texana and subsp. pepo, accessions belonging to the same cultivar-group (fruit shape) associated with one another. Within subsp. pepo, accessions grown for their seeds or that are generalists, used for both seed and fruit consumption, assumed central positions. Specialized accessions, grown exclusively for consumption of their young fruits, or their mature fruit flesh, or seed oil extraction, tended to assume outlying positions, and the different specializations radiated outward from the center in different directions. Accessions of the longest-fruited cultivar-group, Cocozelle, radiated bidirectionally, indicating independent selection events for long fruits in subsp. pepo probably driven by a common desire to consume the young fruits. Among the accessions tested, there was no evidence for crossing between subspecies after domestication.

Li Gong, et al., "Genetic relationships and evolution in Cucurbita pepo (pumpkin, squash, gourd) as revealed by simple sequence repeat polymorphisms" 124(5) Theor. Appl. Genetics 875-891 (November 20, 2011).

The conclusion of the 2011 paper notes that:

Before domestication, Cucurbita pepo evolved into three lineages, subsp. fraterna, which grows wild in northeastern Mexico, subsp. texana, which grows wild in the southeastern United States, and subsp. pepo, which has not been discovered in the wild but may have originated in southern North America. Ornamental cultigens producing the smallest, round, striped fruits are located centrally between subsp. texana and subsp. pepo, suggesting that they are relicts of unknown wild progenitors. No cultigens closely related to subsp. fraterna have been identified. After domestication and long before the arrival of Europeans, subsp. texana evolved into several edible-fruited cultivar-groups characterized by fruit shapes deviating from roundness. In subsp. pepo, the evolution of long-fruited cultivar-groups is more recent and occurred primarily in Europe. Although there is no obvious genetic barrier to crossing among the subspecies, none of the cultivar-groups and none of the accessions examined appears to derive from such crossing.

The body of the 2011 paper notes that:

Cucurbita pepo subsp. texana is divided into distinct sub-clusters​, four of which are based on the edible-fruited cultivar-groups that were defined by fruit shape and named Acorn, Crookneck, Scallop, and Straightneck (Paris 1986). . . . the Scallop Group (T-SC) in the most central position within Cucurbita pepo subsp. texana and, of the edible-fruited cultivar-groups, closest to the wild (T-GT) gourds. Thus, it appears likely that it was the first edible-fruited cultivar-group to have evolved and diversified under the guidance of the pre-Columbian, Native Americans of what is now the United States. Findings of rind fragments of different fruit forms, including lobed, furrowed, and warted, at sites 2,500–3,000 years old in Kentucky, are suggestive of incipient differentiation into the Scallop (T-SC), Acorn (T-AC), and Crookneck (T-CN) Groups (Watson and Yarnell 1966, 1969; Cowan 1997). These three cultivar-groups can be thought of as products of pre-Columbian genetic drift and conservation in isolation that occurred in eastern North America. The Straightneck Group (T-SN) appears to be a much more recent development, judging from the low average GD value among straightneck cultivars (Table 2), consistent with its absence from the historical record prior to the late nineteenth century (Paris 2000a). Earlier results suggested that the Straightneck Group was derived from a cross between a cultivar of the Crookneck Group and a cultivar of the Acorn Group (Paris et al. 2003), but the present results favor a direct derivation from the Crookneck Group. . . .  

The five accessions of the Zucchini Group (ZU) are very closely related, having the lowest within-group GD value. The zucchinis form a distinct sub-cluster, as already observed using other markers. Another sub-cluster is formed by the three accessions representing a market type within the Pumpkin Group (PU), the oil-seed pumpkins, P-PU-GLE, P-PU-STY, and P-PU-WIE. Both, the zucchinis and the oil-seed pumpkins have a short history. The Zucchini Group apparently originated in the environs of Milan in the late nineteenth century (Paris 2000a). The oil-seed pumpkins derive from a recessive, hull-less mutation that occurred in Styria, Austria in the 1880s (Teppner 2000). The Pumpkin Group, the Vegetable Marrow Group (P-VM), and the Cocozelle Group (P-CO), which have considerably longer histories (Paris 2000a), have high within-group GD values and relative high heterozygosities . . . . .  

Even though domestication of subsp. pepo is thought to precede that of subsp. texana by approximately 5,000 years (Smith 2006), selection for deviation from fruit roundness occurred over 2,000 years earlier in subsp. texana, as indicated by rind fragments found in Kentucky.

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Abstract

Genetic relationships among 104 accessions of Cucurbita pepo were assessed from polymorphisms in 134 SSR (microsatellite) and four SCAR loci, yielding a total of 418 alleles, distributed among all 20 linkage groups. Genetic distance values were calculated, a dendrogram constructed, and principal coordinate analyses conducted. The results showed 100 of the accessions as distributed among three clusters representing each of the recognized subspecies, pepo, texana, and fraterna. The remaining four accessions, all having very small, round, striped fruits, assumed central positions between the two cultivated subspecies, pepo and texana, suggesting that they are relicts of undescribed wild ancestors of the two domesticated subspecies. In both, subsp. texana and subsp. pepo, accessions belonging to the same cultivar-group (fruit shape) associated with one another. Within subsp. pepo, accessions grown for their seeds or that are generalists, used for both seed and fruit consumption, assumed central positions. Specialized accessions, grown exclusively for consumption of their young fruits, or their mature fruit flesh, or seed oil extraction, tended to assume outlying positions, and the different specializations radiated outward from the center in different directions. Accessions of the longest-fruited cultivar-group, Cocozelle, radiated bidirectionally, indicating independent selection events for long fruits in subsp. pepo