There is one way to know. Comparing the
haplogroups (
PDF world map here). This is how geneticists know about ancestral origins. The Y-DNA haplogroup trace the paternal line and the mtDNA haplogroup the maternal line.
The
Ainu belong to Y-DNA haplogroup D, which is not found in the Americas. Their closest relatives appear to be the Tibetans. Native Americans belong mainly to Y-DNA haplogroup Q. Some belong to haplogroup C, also found in Japan, but not among the Ainu.
The Ainu mtDNA lineages mainly consist of haplogroup Y (21.6%) and haplogroup M7a (15.7%). Neither is found in the Americas, but rather in China or Siberia. Native American mtDNA haplogroups are A, B, C, D, G and X. All are found in Japan and China, except D (Siberian) and X (European and Siberian).
From this data, I can say that the Ainu are not related to Native Americans. On the other hand non-Ainu Japanese are genetically close to the Native Americans on their maternal line, and share some limited connections on their paternal line.
What is interesting is that mtDNA haplogroup M is absent from America, but present in all East Asia, Ainu included, and it is most common in India. So East Asian have an Indian genetic component lacking in Native Americans.
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