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.