I I have already posted about this The link between Negritos, Papuans and Amerindians!, but the paper by P. Skoglund et al., published online on July 21, 2015 , found a close relationship between the genetic makeup of some Amazonian Native Americans and a group of Oceanian or Austalasian people. Namely, the team found "genome-wide data to show that some Amazonian Native Americans descend partly from a Native American founding population that carried ancestry more closely related to indigenous Australians, New Guineans and Andaman Islanders than to any present-day Eurasians or Native Americans. This signature is not present to the same extent, or at all, in present-day Northern and Central Americans or in a ~12,600-year-old Clovis-associated genome, suggesting a more diverse set of founding populations of the Americas than previously accepted.".
Being beind a paywall, since that first posts I have read other online sources who have accessed the paper found some interesting points to share in this post:
Skoglund et al., found that the Amazonian Amerindians like the Suruí, the Xavante and Karitiana share around 1 or 2% of their genes with aboriginal Andamanese, Papuans and Australians. Furthermore, the 12,600 year-old remains from Anzic, Montana, US, don't have any links to these Australasians suggesting that the Anzic child and modern Amazonians have different origins.
Their explanation is the following:
A simple migration from Melanesia north to Bering and then south into America does not seem likely because there are no traces of Australasian genes along the route. It is improbable that they would have covered such a long route without dallying with the locals and spreading their genes.
Instead they suggest that an ancestral population which is now extinct (that is why their genes cannot be found in Asia), lived in eastern Asia and split into two groups, one that moved south into South East Asia, PNG and Australia and another that marched north across eastern Asia and entered America.
They named these mysterious people as "Population Y" (Y from the Tupi word "Ypykuéra", which means "ancestor").
As I am not constrained by the rigidity of orthodox science, I can suggest that there is a Denisovan link involved in this process:
As Austronesians have a very high share of Denisovan genetic input, the hypothetical "Population Y" may well be the group that admixed with Denisovans, and therefore Denisovan genes in America could have this origin.
An alternative explanation however for the lack of "Population Y" traces in Asia could be that the Denisovans lived both in Asia and America, and admixed with the first wave of humans that went into America and also with the first wave through their Asian homeland: the ancestors of the modern Australasians. Later, they became extinct, but their genes lived on. Later still, Asians with a different genetic make up entered America and swept the first people away. Nowadays only 2% of the old genome survives in the Amazonian forests.
Since the very old hg M mtDNA was found in some ancient native remains in America, but is also found in parts of South East Asia, PNG, India and Tibet. Could this be a signal of the first people to reach America from South East Asia?
We have evidence of humans in Southern Asia aroung 120 kya, a very archaic population of humans; and they probably moved into America and mixed with Denisovans there or in Asia. What is the mtDNA of these people? If the hypothetical Out of Africa move took place earlier, then they could be Haplogroup M. We will have to wait for more evidence.
 Pontus Skoglund, et al. (2015) Genetic evidence for two founding populations of the Americas, Nature 525, 104–108 (03 September 2015) doi:10.1038/nature14895.
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