The five major lineages that make up Native Americans are A, B, C, D, and X. Most scientists believe that America was initially settled from Asia and this is supported by most of the genetic evidence. Most Native Americans are genetically linked to Asia. This fits the long standing theory that the people who populated the two American continents walked across the land bridge that connected Asia with North America during the ice age and later theories that envision boats following the coasts.
The map below shows the distribution of MtDNA lines in America. Lines A through D are the dominant ones and clearly came from Asia. They are distributed throughout North and South America. But X is concentrated in northeast North America. And what is the "other MtDNA" shown for North America?
The map below illustrates the current location of Male "Y" haplogroups passed from father to son. This is the DNA from the indigenous people - Native Americans and Australian Aboriginals. Note that the America's are populated by descendants of three major groups.
Click to view a larger map. https://upload.wikimedia.org/wikipedia/commons/c/ca/World_Map_of_Y-DNA_Haplogroups.png
The map below shows the distribution of the male haplogroup "Q", which is inherited from father to son. Most male Native Americans share this haplogroup and it is clear from the map that it spread from north east Asia into America. It appears to be the signature for the first migrants still reflected in current Native Americans. Both continents were settled.
The map below shows the distribution of the male haplogroup "C3". People with this haplogroup clearly came from Asia and judging from the map, was a later migration into the new world. It did not go further south, probably blocked by earlier migrants to the new world.
Maps are from Wikapedia.