Thursday, October 19, 2017

Early European Farmers Skipped The Baltics

In most of Europe, "Early European Farmers" genetically similar to Anatolian Neolithic farmers and modern Sardinians introduced farming. Then, their economies collapsed eventually in the Middle Neolithic during which populations were infused with hunter-gatherer ancestry, probably due to unsustainable farming practices and climate issues. Then, steppe pastoralists (mostly Indo-European) swept in resulting in major population genetic changes and a rival of societies that took on something close to their current population genetic character in the Late Neolithic/Enolithic/early Bronze Age.

But, this is not what happened in the Baltics. The Early European Farmers never arrived and their first wave of farming arrived with steppe people, according to a new ancient DNA based analysis of the question. Also, while Early European Farmers dramatically replaced local hunter-gatherer populations, Baltic Mesolithic populations had more staying power, so while they had a significant infusion of steppe ancestry into their populations, there is more continuity there between Mesolithic non-farmers and modern populations in these areas.

This could have happened in part because many Baltic hunter-gatherers were maritime fisher-gatherer populations, which are intermediate between terrestrial hunter-gatherer populations and farmers and have more staying power. It could also have happened, in part, because the crops in the Early European Farmer package were ill adapted to high latitude climates. So, the locals had more staying power while the would be incoming Neolithic migrants were at their weakest there, therefore the migration didn't happen.

Insights From Reading Selected ASHG 2017 Abstracts

The abstracts of the conference presentations at the American Society of Human Genetics Conference in Orlando, Florida for 2017 which is currently in progress is available here. It sorts by first digit of the paper number so, for example, 2, 20, 201 and 2001 are all adjacent to each other. Plenary and platform talks have numbers up to 372. Higher numbers are poster-presentations. Some notable papers:

1 African genes governing skin color

1437 Han Chinese genetics overview

2301 Russian haplotypes by geographic area

2304 Two sources from region for mtDNA lineages in Austronesians

2305 Ancestral genetic components in Arabians with attention to Natufians benchmarked against ancient DNA and a Persian Gulf component that doesn't currently have an ancient DNA counterpart

2308 Peruvian genetics showing more diversity of indigenous ancestry than previous studies.

2310 Mongolian DNA and Mongolian introgression into Finns ca. 13th century CE.

2311 Estonian population genetics

2313 Malaysian indigenous populations grew rapidly more distinct despite recent divergence due to natural selection

2314 In Kashmir, India contrary to the male dominated migrant assumption, there is great mtDNA diversity.

2322 Sardinia's population genetic stability since the Neolithic is confirmed with a set of ancient DNA from all intervening time periods.

2323 Decline in effective population and uniparental haplotype diversity in Native Americans quantified

2365 Genetics of Brittany - matches historic rather than current boundaries

2366 Genetics of Ireland - about 70% of territory is mostly Gaelic, about 30% shows admixture with Norman and Norwegian ancestry being most notable. Lines up with historical events.

2357 Easter Islanders have pre-Columbian Native American ancestry but it is derived from other Polynesian islands from which it was settled and not directly.

2324 Origins of genetically Polynesian people in Brazil who died in 19th century before documented migrations redetermined using better reference sets. Original determination had been Cook Islands.

2353 New determination of overall mutation rate in humans.

2354 Mutation rates vary across genome by type of gene.

2357 Lakshudweep Islands were settled from Kerala state

2360 Japan has four genetic clusters, two per language, plus Korean and Amani

2724 Brazilian slaves were almost all from Benin or Bantu with further detail as well

2946 Knockout disorders in Ashkenazi Jews informed by population history

Wednesday, October 18, 2017

Neutron Star Collision Tightens Neutrino Parameter Space UPDATED

The latest big splash in physics, the observation of two neutron stars colliding into each other with both gravity waves and light, provides an independent observation of the Hubble constant that when combined with the Planck data tightens the parameter space of neutrino physics.

The sum of the three neutrino masses goes from less than 1.11 eV with Planck data alone, to less than 0.77 eV with this measurement and the Planck data combined. But, without this new data point, but combined with other data sets, the limitation was already even tighter with combinations as low as 0.11 eV, and the minimum value from neutrino oscillation data is 0.06 eV in a normal hierarchy. It isn't clear how much impact this new data point has on the earlier combination value.

The effective number of neutrino types (Neff) goes from 3.11 ± 0.25 with Planck data alone to 3.09 ± 0.25 with the addition of this measurement. But, as of 2015, the constraint with Planck data and other data sets was 3.04 ± 0.18 (even in 2014 cosmology ruled out sterile neutrinos). Neff equal to 3.046 in a case with the three Standard Model neutrinos and neutrinos with masses of 10 eV or more not counting in the calculation. It isn't entirely clear what the Neutron Star measurement of Hubble's constant adds, if anything, to the combined estimates, but it might, for example, slightly reduce the margin of error which would increase the significance by which the four neutrino case was ruled out. Neff and the Hubble constant are strongly correlated, but the combination value for Hubble's constant is very close to the new value from this observation.

So, the four neutrino case is ruled out at a more than 5.3 sigma level already, which is a threshold for a scientific discovery that there are indeed only three neutrinos with masses of 10 eV or less, ruling out the sterile neutrino hypothesis for a stable sterile neutrino of under 10 eV (when a best fit of potential anomalies from reactors predicts a sterile neutrino mass of about 1 eV also here). A 2015 pre-print on notes that:
The 95% allowed region in parameter space is Neff < 3.7, meff s < 0.52 eV from PlanckTT + lowP + lensing + BAO. This result has important consequences for the sterile neutrino interpretation of short-baseline anomalies. It has been shown that a sterile neutrino with the large mixing angles required to explain reactor anomalies would thermalize rapidly in the early Universe, yielding ∆Neff = 1. The preferred short-baseline solution then corresponds to ms of about 1 eV and ∆Neff = 1 and is strongly excluded (more than 99% confidence) by the above combination of Planck and BAO data.
UPDATE October 19, 2017

* The MINOS and MINOS+ reactor experiments rule out a light sterile neutrino, confirming the cosmology result. The abstract of a new pre-print on their results states that:

"A simultaneous fit to the charged-current muon neutrino and neutral-current neutrino energy spectra in the two detectors yields no evidence for sterile neutrino mixing using a 3+1 model. The most stringent limit to date is set on the mixing parameter sin2θ24 for most values of the sterile neutrino mass-splitting Δm241>104 eV2."

The MINOS data explores a range of values for Δm41 between the lightest mass state and the sterile neutrino mass state of 10 meV to 32,000 meV, where the bounds on the sum of the three neutrino masses from cosmology in the currently experimentally preferred normal hierarchy is 60 meV to 110 meV. For example, the MINOS data shows that:
At fixed values of ∆m241 the data provide limits on the mixing angles θ24 and θ34. At ∆m241 = 0.5 eV2, we find sin2θ24 less than [0.0050 (90% C.L.), 0.0069 (95% C.L.)] and sin2θ34 less than [0.16 (90% C.L.), 0.21 (95% C.L.)].
* Weak boson decays have long ago ruled out the possibility of a number of weakly interacting neutrinos different than three. The number of weakly interacting neutrinos of less than 45 GeV upon Z boson decay is 2.992 ± 0.007 (with a mean value 1.14 sigma from 3) which is consistent with the Standard Model, in a quantity that must have an integer value. The two neutrino and four neutrino hypotheses are ruled out at the 140+ sigma level, when a mere 5 sigma result is considered scientifically definitive.

END UPDATE

Sunday, October 15, 2017

Ancient DNA Refines New World Settlement Paradigm

Overview

new pre-print based on analysis of ancient DNA from a number of far northern populations in North America and Siberia has refined what we know about the waves of pre-Columbian migration to North American after the founding population of American entered North America from the Beringian land bridge not later than about 14,000 BCE.[1] 

There is genetic variation that is found in Canada and the United States, but not in Latin America, which is not attributable to later waves of pre-Columbian migration. This was due either to founder effects in a population that rushed down the Pacific coast over a period of less than 2000 years and became ancestral to all indigenous Americans outside of Canada and the United States, or due to population structure in the original founding population of the Americas.

All pre-Columbian genetic ancestry extant in modern gene pools in the Americas (with the possible exception of part of the ancestry found in certain Amazonian tribes whose source is not well understood which is sometimes described as "Paleo-Asian" [2]) is attributable to this initial founding population (often called "First Americans" in the literature) or two main subsequent migrations from Siberia from genetically related (but not identical) Siberian populations. 

The first wave of subsequent pre-Columbian migration, ca. 3500 BCE (the current pre-print makes the case for an approximate 3000 BCE date [3]) gave rise to the Paleo-Eskimos who ceased to exist as a distinct population around the time that the "Neo-Eskimos" arrived, which is also the source, a few centuries later, of the distinctive genetic ancestry of the Na-Dene people (such as the Tlingit people of Southeast Alaska, and the Apache and Navajo people of the American Southeast), which is otherwise shared with the founding population of the Americas.

The second wave sometime between 1100 BCE and 200 BCE (probably closer to 200 BCE, given the archaeological evidence) gave rise to the Neo-Eskimos such as the Inuits, after substantial admixture with people descended from the founding population of the Americas. (The Na-Dene people were not a source of admixture with the Neo-Eskimos.)

Incidentally, this three wave model had already been predicted based upon archaeological and linguistic evidence several decades before genetic evidence confirmed this model.

There have been a few other well documented instances of much more incidental pre-Columbian contact after the founding population arrived with the Americas (for example, Vikings ca. 1000 CE in Eastern Canada), but none of the other cases left any genetic legacy in the Americas. Also notably, all of those credibly documented contacts post-date the Paleo-Eskimo migration, and all but one doubtful case of a single alleged New World apple seed found in India that was carbon dated to 2000 BCE, post-date both of these migration waves. For example, the Asian War Complex arrives ca. 700 CE, about the same time as the Neo-Eskimos reach Alaska proper, an a previous major bow and arrow technology innovation arrives ca. 400 BCE around the time of first contact between pre-Neo-Eskimos from Asia and and indigenous populations in the Bering Straight. Critically, all First American populations were still isolated from all other modern humans for more than 10,000 years (a time depth that, among other things, is so great that it impossible to reconstruct a proto-Amerind language from known indigenous American languages).

The Story Of The Na-Dene

The genetic distinctiveness of the Na-Dene (a.k.a. Athabaskan) indigenous populations of North America derives from admixture of Paleo-Eskimos in Alaska ca. 3000 BCE plus or minus a few centuries (genetic and archaeological evidence suggests that they arrived ca. 3500 BCE [4], giving rise to the Saqqaq culture and started to admix several centuries later) with indigenous First Americans (whose ancestors arrived over the Beringian land bridge by not later than about 14,000 BCE). The initial admixture percentage in ancient Northern Athabaskans was roughly 25%-40%. Over time, the Paleo-Eskimo admixture percentage in the Na-Dene has been diluted to about 10%, but all Na-Dene populations have this ancestry which is almost completely absent from non-Na-Dene language speakers.

Genetic evidence also supports the Dene-Yeniseian linguistic hypothesis that the Na-Dene languages have a linguistic family relationship with the Yeniseian language family of Siberia of which the sole surviving language is the Ket language. Specifically, ancient DNA from a population in the Ust'-Belaya culture of Chukotkan in Siberia, which is ancestral to the Paleo-Eskimos, shows evidence of genetic relatedness to both the Paleo-Eskimos and a western Siberian group related to Kets. The pre-print notes that: 
striking parallels in archaeological and genetic results suggest that admixture between proto-Paleo-Eskimos and Siberian lineages in Chukotka took place not long after they diverged [ca. 4300 BCE], indicating that cultural contact between these groups at this time almost certainly occurred as well. This result has implications for archaeology and historical linguistics[.]
At least two "push factors" drove Na-Dene tribes such as the Navajo to migrate to the American Southwest around 900 CE, and may have also been involved in the migration of the Tlingit Na-Dene tribes to southeastern Alaska and Pacific coastal Canada. One was the arrival of "Neo-Eskimos" (e.g. the founding population of the Inuits who were part of the Birnirk and Thule cultures) in western Alaska ca. 650 CE to 850 CE. The other was a massive volcanic ash fall ca. 900 CE. There was little or no Na-Dene genetic introgression into Neo-Eskimo populations. 

In the American Southwest, there was also a "pull factor" which was the control vacuum created when the society of the ancient Puebloan people (a.k.a. the Anasazi) collapsed, in part due to a major drought associated with the Medieval Climate Anomaly (which quite possibly was related, in part, to the volcanic eruptions that took place at about the same time that the MCA began) that may have partially encouraged Na-Dene people who had already migrated to the Canadian heartland to migrate South, or may have made them more successful as a potentially competing collapsed when, or not long after, they arrived.

It is also worth noting that there were major innovations in bow and arrow technology ca. 2500 BCE, which had previously been stagnant since 10,000 BCE, which might have coincided with the arrival of the Paleo-Eskimos and the increasing prevalence of the Arctic Small Tool tradition.

The Story of the Modern Eskimos

Some members of the population the Siberian population ancestral to the Paleo-Eskimos migrated to North America. Others remained in Siberia and gave rise to a sub-population ca. 1500 BCE (about 1500 years after the first wave admixed with the Na-Dene) that was ancestral to modern "Neo-Eskimos" such as the Inuits who arrived in western Alaska ca. 650 CE to 850 CE and are known to archaeologists as the Birnirk and Thule cultures. About 43% of the modern Neo-Eskimo population's ancestry is attributable Asian migrants from this population and this population is also the source of mtDNA D2a in Neo-Eskimos. 

The balance of Neo-Eskimo ancestry [5], arises from northern non-Na-Dene descendants of the first wave of migrants to North America, and in particular, from descendants of the indigenous southwestern Alaska and Kodiak Island Ocean Bay tradition (which flourished ca. 4800 BCE to 2500 BCE) in which a lot of the technological innovations involving year round maritime hunting were invented. In contrast, early "Paleo-Eskimo people used marine resources on a seasonal basis only, depended for the most part on hunting caribou and muskox, and lacked sophisticated hunting gear that allowed the later Inuit to become specialized in whaling." Thus, while the new influx of genes and their language had Asian origins, their maritime hunting technologies were made in North America.

The admixture that gave rise to the modern Neo-Eskimo population had already substantially run its course by 200 CE when ancient DNA reveals an already admixed Neo-Eskimo who was part of the Old Bering Sea culture which commenced ca. 200 BCE.

The admixture that gave rise to the ethnogenesis of the Neo-Eskimos predated the Ipiutak culture of western Alaska which emerged ca. 300 CE.

It is possible that some or all of the admixture and ethnogenesis that gave rise to the Neo-Eskimos took place in the Old Whaling culture of western Alaska (ca. 1100 BCE to 700 BCE), the Choris culture of western Alaska (ca. 700 BCE to 500 BCE) or the Norton culture of western Alaska (ca. 500 BCE to 200 BCE). There isn't enough ancient DNA data available to be more specific. Archaeological data tends to support a date at the more recent end of that range, such as the tail end of the Norton culture [6].

End notes and language from the body text of the paper supporting this summary, with editorial emphasis, additional hyperlinks to prior posts at this blog, and headings, appear below.

Saturday, October 14, 2017

Cosmological Inflation Still Bad Science UPDATED

Sabine's latest blog post explains deep problems with the theory (really an infinite class of theories) of cosmological inflation research.

Basically, it is underdetermined and can't predict anything meaningful.

UPDATE October 18, 2017

A follow up blog post explains that the flatness problem that inflation is commonly described as solving comes from an unjustified and probably unreasonable assumption about initial conditions.

END UPDATE

Friday, October 13, 2017

Back To Basics In High Energy Physics UPDATED

Usually, the headlines in physics go to people who are proposing or discovering "new Physics", but an important part of the high energy physics enterprise is constantly pushing for more precise measurements of quantities involved in plain old Standard Model physics that has been settled science for decades. Today's research results are mostly of that variety:

Top Quark Measurements:

* The DZero collaboration at the now completed Tevatron experiment released another review of its old data regarding the mass of the top quark. Bottom line:
The most precise single measurement at the Tevatron of mt = 174.98 ± 0.58(stat+JES) ± 0.49(syst) GeV is performed by the D0 Collaboration in the `+jets channel, corresponding to a relative precision of 0.43%. The combination with all other measurements from the D0 experiment results in mt = 174.95±0.40(stat)±0.63(syst) GeV. The Tevatron combination yields mt = 174.30±0.35(stat)± 0.54(syst) GeV, which corresponds to a relative precision of 0.37%.
The directly measured top quark mass according to the Particle Data Group is as follows, based upon a combined CMS measurement, a combined ATLAS measurement and a combined Tevatron measurement:

OUR AVERAGE  Error includes scale factor of 1.6.
 1
AABOUD
2016T
ATLScombination of ATLAS
  2
KHACHATRYAN
2016AK
CMScombination of CMS
  3
TEVEWWG
2016
TEVATevatron combination

The top quark mass measured indirectly via cross-section measurements per PDG is as follows:

OUR AVERAGE
 ± 1
ABAZOV
2016F
D0 , +jets channels
 2
KHACHATRYAN
2016AW
CMSe + μ + T + 0j
 3
AAD
2015BW
ATLS+T+5j (2b-tag)
 4
AAD
2014AY
ATLSpp at s = 7, 8 TeV

"An extended Koide's rule estimate of the top quark mass using only the electron and muon masses as inputs, predicted a top quark mass of 173.263947 ± 0.000006 GeV", via this prior blog post, which is very close to the best fit measured value.

As previously noted in a December 16, 2016 blog post at this blog:
If the the sum of the square of the boson masses equals the sum of the square of the fermion masses equals one half of the Higgs vacuum expectation value, the implied top quark mass is 174.03 GeV if pole masses of the quarks are used, and 174.05 GeV if MS masses at typical scales are used. . . . 
The expected value of the top mass from the formula that the sum of the square of each of the fundamental particle masses equals the square of the Higgs vaccum expectation value (a less stringent condition because the fermion and boson masses don't have to balance), given the global average Higgs boson mass measurement (and using a global fit value of 80.376 GeV for the W boson rather than the PDG value) is 173.73 GeV. The top quark mass can be a little lighter in this scenario because the global average measured value of the Higgs boson mass is a bit heavier than under the more stringent condition.
Both of the predictions from these phenomenological hypotheses are a bit heavier than the currently measured top quark masses as the LHC measurements have turned out to be smaller than the Tevatron measurements which are quite close to these expected values. But, the scatter in the various measurements is still broad enough that these values cannot be ruled out.

UPDATE October 18, 2017: A new review of ATLAS top quark mass measurement is available, but most, if not all are already incorporated in the PDG global weighted average:
Results of top-quark mass measurements in the di-lepton and the all-jets top-antitop decay channels with the ATLAS detector are presented. The measurements are obtained using proton-proton collisions at a centre-of-mass energy s = 8 TeV at the CERN Large Hadron Collider. The data set used corresponds to an integrated luminosity of 20.2 fb1. The top-quark mass in the di-lepton channel is measured to be 172.99 ± 0.41 (stat.) ± 0.74 (syst.) GeV. In the all-jets analysis, the top-quark mass is measured to be 173.72 ± 0.55 (stat.) ± 1.01 (syst.) GeV. In addition, the top-quark pole mass is determined from inclusive cross-section measurements in the top-antitop di-lepton decay channel with the ATLAS detector. The measurements are obtained using data at s = 7 TeV and s = 8 TeV corresponding to an integrated luminosity of 4.6 fb1 and 20.2 fb1 respectively. The top-quark pole mass is measured to be 172.9+2.52.6GeV.
Teresa Barillari, "Top-quark mass and top-quark pole mass measurements with the ATLAS detector"(October 16, 2017). END UPDATE.

* The ATLAS and CMS experiments at the Large Hadron Collider (LHC) have released a summary of their findings regarding top quark properties. Unsurprisingly, they are consistent with Standard Model expectations in all respects and strictly limit anomalies in the transition from the top quark to the bottom quark via the weak force as the accuracy of the measurement of this quantity improves. Several measurements were made and two of the easiest to summarize results were as follows:

W Boson Helicity In Top Quark Decays
The W-boson helicity fractions (left-handed, right-handed and longitudinal) are defined as FL,R,0 = ΓL,R,0/ΓTotal, where ΓL,R,0 are the partial decay widths in left-handed, right-handed, and longitudinal helicity states respectively, with ΓTotal being the total decay width. The SM next-tonext-to-leading order (NNLO) calculations [4] including the electroweak effects predict the values of FL = 0.311±0.005, FR = 0.0017±0.0001 and F0 = 0.687±0.005, for a top quark mass of 172.8±1.3 GeV. 
The crude average of the CMS and ATLAS measurements (which do be exactly right should be error weighted and should include the error bars of the combined result) are as follows:

FL=0.311 (v. predicted value 0.311), FR=0.006 (v. predicted value 0.0017), and F0=0.695 (v. predicted value 0.687).

The results for FL and F0 are within the combined theoretical uncertainty of the Standard Model prediction even before considering experimental uncertainty.

The result for FR is within the experimental uncertainty of Standard Model prediction at the two sigma level. Also, keep in mind that FL, FR and F0 are not independent of each other and involve just two degrees of freedom, not three, but the crude average measurements above don't globally fit the data to reflect that fact.

Combining the ATLAS and CMS results properly, on an error weighted basis and doing a global, would give a better result, because the measurement that is closer to the predicted value has a significantly lower margin of error and because the experimental measurements of FR and F0 combined would each be reduced proportionately by a little bit in a global fit since FL+FR+F0 estimated independently slightly exceed 1.0 which must be true as a consequence of the way those variables are defined. The deviation if it was all done properly would be a bit more than one sigma.

Top Quark Decay Width

The Standard Model prediction for the top quark decay width (which as explained in a previous post at this blog is good global measure of deviations from the Standard Model) is ΓSM=1.324 GeV for mt=172.5 GeV.  The CMS measurement of the decay width of the top quark is Γt = 1.36 ± 0.02(stat)+0.14 −0.11 (syst) GeV, which agrees with the Standard Model prediction at the 0.3 sigma level.

The CMS boundary on the top mass decay width is tighter than the most recent ATLAS measurement of:
Γt = 1.76 ± 0.33 (stat.) +0.79 −0.68 (syst.) GeV = 1.76+0.86 −0.76 GeV.
The Charm Quark Mass

A previous determination of the charm quark mass at a 3 GeV energy scale was updated based upon late breaking new experimental data. Bottom line: "Our final result for the MS charm-quark mass reads mc(3 GeV) = 0.993 ± 0.008 GeV and mc(mc) = 1.279 ± 0.008 GeV."

Higgs Boson Measurements

The CMS experiment at the LHC has released its latest experimental data on decays of Higgs bosons to W bosons, to tau lepton pairs, and to muon pairs. It finds that:
the combined observed limit for 7 and 8 TeV [at the 95% confidence level] is 7.4, while the background-only expected limit is 6.5 +2.8 −1.9 . This corresponds to an observed upper limit on B(H → µµ) of 0.0016, assuming the SM cross section. The best fit value of the signal strength for a Higgs boson mass of 125 GeV is 0.8 +3.5 −3.4.
Given the large margin of error, the biggest surprise is that it is so close to the Standard Model expectation (0.059 sigma from the expected value in the Standard Model), which suggests that either the error in this measurement is probably greatly overestimated, or that CMS just got lucky, or both.

Analysis

None of the results are particularly surprising, but greater precision in these measurements of fundamental Standard Model physics quantities makes all other high energy physics work more accurate and broadly constrains all forms of beyond the Standard Model physics.