Towards a new history and geography of human genes informed by ancient DNA.

[Argang]

This paper doesn't have much new information, but stresses the importance of using ancient genomes in ancestry studies. They also model world populations as mixes of modern populations that are supposed to be proxies for ancient ones. Europeans such as Orcadians, northern Russians, Belorussians and French for example fit best as Sardinian + Karitiana (Neolithic Farmer + ANE) mixes.

http://biorxiv.org/content/biorxiv/early/2014/03/21/003517.full.pdf



Genetic information contains a record of the history of our species, and technological advances have transformed our ability to access this record. Many studies have used genome-wide data from populations today to learn about the peopling of the globe and subsequent adaptation to local conditions. Implicit in this research is the assumption that the geographic locations of people today are informative about the geographic locations of their ancestors in the distant past. However, it is now clear that long-range migration, admixture and population replacement have been the rule rather than the exception in human history. In light of this, we argue that it is time to critically re-evaluate current views of the peopling of the globe and the importance of natural selection in determining the geographic distribution of phenotypes. We specifically highlight the transformative potential of ancient DNA. By accessing the genetic make-up of populations living at archaeologically-known times and places, ancient DNA makes it possible to directly track migrations and responses to natural selection.

[Argang]

Fits for european populations can be found from supplementary data (http://biorxiv.org/content/biorxiv/suppl/2014/03/21/003517.DC1/003517-1.pdf). Quite uniform results:

Utah American : Karitiana Sardinian
Tuscan : Karitiana Sardinian
France : Karitiana Sardinian
Italy : Karitiana Sardinian
Orcadian : Karitiana Sardinian
Russian : Karitiana Sardinian
Adygei : Karitiana Sardinian

[Argang]

The impact of whole-genome sequencing on the reconstruction of human population history (http://www.nature.com/nrg/journal/v15/n3/abs/nrg3625.html)
A somewhat related paper that's unfortunately not open access.

Abstract:

Examining patterns of molecular genetic variation in both modern-day and ancient humans has proved to be a powerful approach to learn about our origins. Rapid advances in DNA sequencing technology have allowed us to characterize increasing amounts of genomic information. Although this clearly provides unprecedented power for inference, it also introduces more complexity into the way we use and interpret such data. Here, we review ongoing debates that have been influenced by improvements in our ability to sequence DNA and discuss some of the analytical challenges that need to be overcome in order to fully exploit the rich historical information that is contained in the entirety of the human genome.

Unsurprisingly the ancient hunter-gatherer genomes are on the same level with Northern Baltic populations on Dimension 1 which has more of the variation. Like La Brana they seem to also have a secondary northwest european dimension. Dimension 1 is a typical North/South euro divide, while Dimension 2 seems to be "British Isles vs others" since more eastern Finns and Tuscans are equally distant from UK while west Finns and Iberians are about the same. The farmers seem to quite close to South Europeans.
http://www.nature.com/nrg/journal/v15/n3/images/nrg3625-f3.jpg

[Argang]

Svante Pääbo announced that his team has managed to get a good sequence of the genome of a 45 000 years old Homo Sapiens from Siberia, by far the oldest of ancient genomes sequenced so far. The research itself isn't published yet, but this individual lived at the time while Neanderthals still existed, and they announced it had a larger amount of their DNA than today's humans.
http://www.sciencemag.org/content/343/6178/1417.summary
http://4.bp.blogspot.com/-1kTNEheaWSQ/UzTMLl0EiYI/AAAAAAAAJis/Nzqj5tDUq0w/s1600/F1.large.jpg


Because all living people in Europe and Asia carry roughly the same amount of Neandertal DNA, Pääbo's team thought that the interbreeding probably took place in the Middle East, as moderns first made their way out of Africa. Middle Eastern Neandertal sites are close to Skhul and Qafzeh, so some researchers suspected that those populations were the ones that mingled. But the team's analysis favors a more recent rendezvous. The femur belonged to an H. sapiens man who had slightly more Neandertal DNA, distributed in different parts of his genome, than do living Europeans and Asians. His Neandertal DNA is also concentrated into longer chunks than in living people, Pääbo reported. That indicates that the sequences were recently introduced: With each passing generation, any new segment of DNA gets broken up into shorter chunks as chromosomes from each parent cross over and exchange DNA. Both features of the Neandertal DNA in the femur suggest that the Ust-Ishim man lived soon after the interbreeding, which Pääbo estimated at 50,000 to 60,000 years ago.

[Black Wolf]

Did they manage to get either Y-DNA or mtDNA at all from the Ust-Ishim man does anyone know?

[Argang]

Did they manage to get either Y-DNA or mtDNA at all from the Ust-Ishim man does anyone know?

The article didn't mention it and neither did Dienekes. So either they didn't get haplogroups or are holding onto that as a surprise.

Its Y-DNA is anyone's guess, it could be P or K, but also something earlier like F, or even C like La Braña. I think it's too early for R.

[Kale]

I thought it said entire nuclear genome sequenced? Which would mean we have a y-dna.

[Argang]

I thought it said entire nuclear genome sequenced? Which would mean we have a y-dna.

If that's the case they're certainly going to sit on the data on it until their results are published, which could take time.

The genome's so old that F and C are starting to look most likely, I did suggest P in a previous post but apparently even that is estimated to be younger.