A paper (Morten Rasmussen et al., 2009)  reports the sequencing of the genome of a male from Greenland; it was obtained froma a hair (about 4,000 years old) that was found in the permafrost. The man belonged to a wave that peopled the New World long after the original and older migration of modern Amerindians.
The interesting part (from my perspective) is the information regarding Native Americans and how different they are from their purported Siberian ancestors.
The following image (Adapted from Fig. 3 in ) and, just by looking at it you can see some intriguing trends:
Part (b) of the figure (upper right corner of the image) shows a clear distribution where Siberians and East Asians are found on the upper branch, Europeans on the Right tip, where upper and lower branches meet, and Southern and Meso-American Natives are found on the bottom left tip of the lower branch.
It is very evident by the distance between them, the vector orientation and their placement in different branches, that current Siberians and Asians are not related to modern Amerindians.
Part (c) shows a plot generated by the ADMIXTURE39 algorithm with K = 5. It shows individuals from 35 extant Eurasian and American populations which are represented by stacked columns with five ancestry proportions (y axis indicates the fraction of each of the five inferred ancestral groups).
We can see that:
- (Blue color). There is an important western Eurasian component admixed into Siberians, Northernmost North Americans and Greenlanders. This drops off sharply with a North to South cline for the other Amerindian populations.
- (Brown or Burgundy color). The Amerindian component is prevalent with a decreasing South - North Cline, among all Native American groups. And is also found in minimum fractions among Chuckchis, Tuvinians, Altai, Selkups and Kets. (We will look into this further down)
- (Pale Yellow). Found in minimum frequencies in Eastern Siberia, it incrases to nearly 90% among West Beringian Koryaks and Chukchis, with a strong prevalence among Arctic Americans and Na-Dene natives. It drops off with a north to south cline from around 40% in Na-Dene to a <10% fraction among Southern Amerindians.
- The other components are absent among South American Natives.Orange, which is prevalent among Chinese, Japanese and East Asians, drops off towards Eastern Siberia. Dark Yellow, which grows with a West to East cline and is maximum in Central and Northern Siberia.
The Amerindian signature in Asia
The "brown component" found in small frequencies in Asia is quite interesting and exactly the same pattern appears in another paper (Li et al., 208) ; In this case the sample includes populations from African, Southern Asian, PNG and the Middle East. Below is its Figure 1 A:
The image indicates the ancestry of different populations at K = 7 (seven inferred ancestral groups). 
We see that the pattern is repeated and that the Amerindian component (Violet) appears predominantly (>90%) in South America (with a slight admixture of European and even less components from other regions).
The Amerindian "violet color" reappears in East Asia among the Yakut, but with extremely small frequencies among the: Oroquen of Heilongjiang (China), the neighboring Daur of Mongolia, Hazara (Afghanistan) and Mongols. It reappears again at relatively higher frequencies among the Russians.
Why do all these Eurasian people have a tiny proportion of Amerindian in them?
The accepted theory is the following:
Modern Humans reached Siberia relatively late, the rest of the Old World was already peopled. The icy Siberian regions had effectively formed a barrier to all hominins until the superior skills of modern Homo sapiens (invention of needles to sew fur clothes and the mastery of glacial-condition survival skills) breached that last barrier.
This enabled Siberians from Central Asia to trek out on a Northeastern course, reach Beringia and stay there about 5,000 years during the peak of the last Ice Age, hunting mammoths and other tundra herbivores. During this time they became quite distinct from a genetic point of view from the relatives that stayed behind in Siberia. Then during deglaciation they packed their tents and gear and rapidly marched on into the vast and empty New World occupying it in less than 2,000 years.
A second wave of migrants admixed with the first, bringing some more recent Siberian alleles which are found among Na-Dene, Innuit and other North American natives. South America remained free from this admixture.
So, any similarity between Siberians and Amerindians is due to their common ancestry. There are differences of course, but these are due to the long sojourn in Beringia which gave time for unique Native American alleles to appear and also for founder effect (only a few clans of Siberians reached Beringia, so their set of genes was rather limited) and bottleneck (some clans died out and their lineages with them, further depleting Amerindian genetic diversity) to act and further separate Americans from Asians.
By the way, these people expanded into America in small isolated groups that did not mix frequently with their neighbors, so they developed in a very short period of time, hundreds of unique languages and their genomes took disparate courses which due to drift made them appear different, but actually all sharing the same recent Asian origin.
Last of all, enslaved Africans and Europeans admixed after 1492 C.E. as a consequence of the discovery of America by Europeans so any odd European or African genes found among Amerindians (even the most isolated groups) are due to this recent admxiture.
Another unorthodox view
The model outlined above does not even consider the possibility of a pre-sapiens peopling of America. The H. habilis from Dmanisi in Georgia, the H. erectus from China or even Neanderthals and Denisovans from Altai, could have continued onwards into America, but archaic sites with Acheulean or Mousterian tools are lightly dismissed by mainstream science as geofacts or of recent manufacture.
The recency in the peopling in America is taken as a proven fact and the data are used by other branches of science (i.e. genetics) when calibrating their methods. As seen in previous posts, the late peopling of America and Siberia is accepted without questioning. This in turn implies that Old World populations have "deeper evolutionary histories", and Amerindians, in contrast are "recent".
The bottleneck and founder effects are generally assumed to have taken place prior to or during the Beringian Standstill, thus restricting the gene pool that entered America. I have not seen papers that explicitly recognize that America was peopled by a popuation with a wide spectrum of alleles and that they became extinct due to the negative impact of mass deaths caused by disease, war and over exploitation of natives after the Discovery and Conquest of America. This overlooked event was an exceptionally strong force even as recently as the late 1800s, and early 1900s.
As an example, the population of Yaghans or Yamana, canoe people living in the fjords of Southern Tierra del Fuego and the Selknam hunter gatherers of the Fuegian mainland, dropped dramatically after contact with Europeans:
The Yaghans passed from 3,000 to 100 people between 1850 and 1916; in 1995 only 75 people of admixed Yaghan origin survived. The Selknam decreased from 3,500 to 800 during the same period, today only 696 persons of mixed Selknam descent survive. Whooping cough, tuberculosis, small pox and VD wiped them out.
These were the real bottlenecks that wiped out people who had lived in isolation from Old World illnesses for milennia. But let's get back to our main subject. The alternative theory for the peopling of America.
What to Yakuts, Oroquen, Daur, Hazara, Mongols, Russians, Chuckchis, Tuvinians, Altai, Selkups and Kets have in common that allows them to have minute quantities of Amerindian ancestry?
The map I prepared (see below) shows their approximate geographic location and the figure inside each oval is the rough percentage of Amerindian ancestry in each group (it indicates the average value within each population):
We see a high frequency of Amerindian ancestry among Chukchis, Kets and Selkups. And a drop towards the south: Altai, China, Mongolia and the Hadzas. Russians: it is hard to define a location for them since we do not have the data about where the samples were taken. But the value is high and uniformly distributed among them.
I believe that there was a back-migration from America into Eastern Siberia. This accounts for the high content among Chukchis (red arrow A in map).
The dispersal advanced further into East Asia along a northern corridor since to the south mountain ranges (Cherskiy and Kolyma) along the coast blocked the way. The route then crossed the Verkhoyansk Range and reached the Lena River Basin, and, further West, the Yenisei River Basin where it admixed with the aboriginal people living there. (red arrows B in map). To the south, the Iablonovy and Stanovoy Mountains blocked their advance into Manchuria, Mongolia and China. This was the maximum advance of these "Out-Of-America" migrants. (shaded pale red in map).
Much later, the current populations of Selkups, Yakuts and Kets moved north and east into these regions and admixed with these aboriginals, incorporating the Amerindian alleles into their genome (blue arrows in map).
And then, much more recently, further mixing towards the South along the Amur and then West through Mongolia incorporated these genes into the Oroqen, Daur and Mongols. Additional dispersal towards Altai and into Russia took place along the Northernmost Silk Road (Euasian Steppe Road); similar dispersal incorporated them into the Hadza in Afghanistan. (green arrows in map).
But who are these Selkups, Yakuts and Kets?
The Turkic people
The homeland of the Turkic people and their language is in the Altai region, where proto Turkic appeared ca. 400 BC. It expanded from there: the Tuvans and Sakha (or Yakut) moving East and Northwards, and others moving west around Aral, the Caspian and into Asia Minor (finally settling in Turkey).
Let's take a look at the Asians who carry these American components:
The Sakha or Yakut left their Altai homeland forced by their neighbors. They advanced along the Lena River towards the northeastern forests of Siberia. They admixed with the local natives (some of which carried the ancient Amerindian component) and also with mongol people, which have left a strong Mongol - East Asian component in them.
The Kets, also from the Altai, and also forced north due to conflict with belicose neighbors. They have a very strong Amerindian component and also, the highest frequency of Y chromosome haplogroup Q in all of Asia (93.7%), which is only found among Amerindians. Currently they are a small population (<1,500 people) yet many name places in Siberia are Ket. They are linked to the later wave that peopled America through the Na-Dene - Yeniseian languages.
The Selkups (currently about 4,300 people) have the second-highest frequency of haplogroup Q in Asia (66.4%). They were not originally from Siberia, they migrated East from the Urals and mixed with Turkic elements in the Altai area and also with the aboriginal peoples of the Yeniseian region (Siberia) who carried the Amerindian alleles. 
The Y-chromosome Q haplogroup mentioned above is very interesting and worthy of the second Part of this post.
 Morten Rasmussen et al., (2009). Ancient human genome sequence of an extinct Palaeo-Eskimo. Nature 463, 757-762 (11 February 2010) | doi :10.1038/nature08835.
 Li JZ, Absher DM, Tang H et al., (2008). Worldwide human relationships inferred from genome-wide patterns of variation. Science 2008; 319: 1100–1104
 The Turkic Languages in a Nutshell
 The Red Book of the Peoples of the Russian Empire
 Tatiana M. Karafet et al., (2002). High Levels of Y-Chromosome Differentiation among Native Siberian Populations and the Genetic Signature of a Boreal Hunter-Gatherer Way of Life. Human Biology, December 2002, v. 74, no. 6, pp. 761–789.
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