Saturday, March 25, 2017

Thursday, March 23, 2017

Mediterranean Farmers Took Local Mesolithic Era Migration Wives

Much of the modern mtDNA of Europe (with exception of mtDNA U and perhaps mtDNA V) is derived from mtDNA clades in West Asia and Southwest Asia. The latest study focused on clades of mtDNA J and mtDNA T in modern Europeans, dating their formative periods via mutation rate dating and phylogeny.

In Central Europe and Iberia, these Near Eastern mtDNA clades arrived with more or less gender balanced first farmer families in the Neolithic revolution. 

But, in central and eastern Mediterranean Europe (presumably Greece, the Balkans, Italy and Southern France), these mtDNA clades arrived in the Mesolithic era, after the Younger Dryas ice age, but before farming was introduced. Local women were then integrated into the farming societies that arrived later in the Mediterranean Neolithic revolution (mostly notably the Cardial Pottery Neolithic).
Important gaps remain in our understanding of the spread of farming into Europe, due partly to apparent contradictions between studies of contemporary genetic variation and ancient DNA. 
It seems clear that farming was introduced into central, northern, and eastern Europe from the south by pioneer colonization. It is often argued that these dispersals originated in the Near East, where the potential source genetic pool resembles that of the early European farmers, but clear ancient DNA evidence from Mediterranean Europe is lacking, and there are suggestions that Mediterranean Europe may have resembled the Near East more than the rest of Europe in the Mesolithic. 
Here, we test this proposal by dating mitogenome founder lineages from the Near East in different regions of Europe. We find that whereas the lineages date mainly to the Neolithic in central Europe and Iberia, they largely date to the Late Glacial period in central/eastern Mediterranean Europe. This supports a scenario in which the genetic pool of Mediterranean Europe was partly a result of Late Glacial expansions from a Near Eastern refuge, and that this formed an important source pool for subsequent Neolithic expansions into the rest of Europe.
Joana B. Pereira. et al., "Reconciling evidence from ancient and contemporary genomes: a major source for the European Neolithic within Mediterranean Europe" Proceedings of the Royal Society B (Biology) (March 22, 2017).

Further discussion of the body text of this paper can be found at Bernard's blog (in French).

The Limits Of Consumer Genomic Ancestry Reports

Razib has a nice discussion of the limitations of ancestry assignment methods in consumer genomic products like 23andMe. He makes a couple of key points:

* South Asia has ten times as much intra-regional variation as Northern Europe, but genomics companies currently make little effort to disaggregate this variation outside Europe.

* Consumer genomic companies are in a bind, because the genomic structure of Europe doesn't track the modern national boundaries well. 

Some of the genomic structure of Europe is more clear at a sub-national region level that may cross national boundaries, and some of it is related to events too deep in prehistory to to well known to the general public (e.g. the hunter-gather, first wave Neolithic, and early Bronze Age population shifts plus some minor or only locally significant matters like admixture arising during European colonial empire periods, and major population disruptions in Austria-Hungary). But, without a lot of context, those distinctions don't make much sense to typical personal genomics company customers.


Still No Evidence Of SUSY

Supersymmetry (i.e. SUSY) is not supported by any experimental evidence that distinguishes it from the Standard Model, and the exclusions are far above the weak scale where it was expected to manifest itself. 
This week results are being presented by the LHC experiments at the Moriond (twitter here) and Aspen conferences. While these so far have not been getting much publicity from CERN or in the media, they are quite significant, as first results from an analysis of the full dataset from the 2015+2016 run at 13 TeV, This is nearly the design energy (14 TeV) and a significant amount of data (36 inverse fb/experiment). The target for this year’s run (physics to start in June) is another 45 inverse fb and we’ll not start to hear about results from that until a year or so from now. For 14 TeV and significantly larger amounts of data, the wait will be until 2021 or so. 
The results on searches for supersymmetry reported this week have all been negative, further pushing up the limits on possible masses of conjectured superparticles. Typical limits on gluino masses are now about 2.0 TeV (see here for the latest), up from about 1.8 TeV last summer (see here). ATLAS results are being posted here, and I believe CMS results will appear here.
From here.

In other news from these conferences in progress, there are no newly announced Higgs boson mass or width results, and the experimentally measured fit of the observed Higgs boson couplings to those predicted by the Standard Model remains very tight (comfortably within one standard deviation of the expected value overall).

No significant BSM physics of any kind has been observed definitively at the LHC, although a handful of moderate significance anomalies have been noted that might or might not amount to anything. None of the anomalies are easy and obvious fits to popular BSM theories akin to SUSY.