Here is a good introduction into the genetics of Indigenous Americans.
The genetic history of indigenous peoples of the Americas primarily focuses on Human Y-chromosome DNA haplogroups and Human mitochondrial DNA haplogroups. Autosomal"atDNA" markers are also used, but differ from mtDNA or Y-DNA in that they overlap significantly. The genetic pattern indicates Indigenous Amerindians experienced two very distinctive genetic episodes; first with the initial peopling of the Americas, and secondly with European colonization of the Americas. The former is the determinant factor for the number of gene lineages, zygosity mutations and founding haplotypes present in today's Indigenous Amerindian populations.