Who settled the Americas first? The Asians certainly did according to all reasonable theories. The possibilities seemed limited but now South American natives have been much more carefully and extensively studied than ever before by Daniel Turbon and his many colleagues from Europe and the Americas. You can read their whole detailed research at PLoS ONE Genetics.
Y chromosomal markers from 1011 males within 50 tribal groups show very distinctive genetics compared to other Americans. This supports those theories that indicate multiple migrations from various locations, "rapid peopling" and the long isolation of small tribal populations. A major part of the findings in this paper is the existence of a founder lineage in the NW of South America (Ecuador.)
This "haplogroup" is related to common Asian lineages, but not any nearby North American groups. The only explanations for this so far have been a coastal or Pacific route for the ancestors of these people. Archaeology and the origins of the haplogroup about 6000 years ago support these explanations.
Humans colonise by creating a pattern of genetic variation suiting geography and their language. This is because gene flow is conducted by these two factors, meaning any abrupt change should be simply observed within language or decided by geography. Slav and Latin-based language groups are typical examples in Europe, indicated by Y chromosome markers. Strangely, the maternal mtDNA lineages aren't influenced in the same way.
Beringia was supposedly the original source of proto-Americans. Many possibilities could have influenced colonisation at the Panama isthmus or when the vast Amazon basin presented its geography to the first observers. The colonisation should have been rapid, especially considering the archaeological remains, with a date of 13-14,000 years for both North and South American remains.
Only an Asian origin can be reasonably claimed, but Polynesians and others can't be entirely excluded. After colonisation, the most reduced genetic diversity and the strongest differentiation was within the natives of the east of South America. Do geographical and language (from 26 different language groups) considerations dominate South American variation?
The answer is that it does not and this supports colonisation that somehow avoid North America, by using a trans-Pacific or coastal migration! The most incongruous part of the findings is the report of similarities between pottery from the middle Jomon culture of Kyushu and Ecuadorian shore culture from the Valdivian culture, both estimated at 4400 to 3300BC. Whether such trading relations of ethnic history could have taken place is unlikely on the surface. We can only hope more investigation into such remarkable claims are fruitful.