Other genetic markers anthropologists can use to track the potential migration history of indigenous people in the Americas are the uniparentally inherited genetic materal: Y chromosomes and mitochondrial DNA. Mitochondrial DNA (mtDNA) is inherited from a mother to all her descendents while the Y chromosome is paternally inherited. The similar mode of inheritance between mtDNA and the Y chromosome allows anthropologist’s to pick either marker and hold to a high degree of certainty that they are seeing a single lineage into the past, but mtDNA and Y chromosomes rarely have an identical past or show congruent population variation due to discrepancies in sex variation of founding populations, sex-biased post-Colombian interaction between Native populations and Europeans, or random gene flow (Yunis, 2013, pp. 329-335). This incongruence is found in Native American populations and highlights how every genetic marker, down to every gene, has a unique genetic history. To fit within the parameters of this paper only studies focusing on the Y chromosome of indigenous American populations will be discussed.
The Y chromosome is the sex chromosome carried by all human males; it is inherited from father to son. Males have two sex chromosomes, but they are not synonymous like they are in females (XX). Instead, males have one X, inherited from their mother, and one Y from their father. The X and the Y recombine in a very limited number of regions with a majority of the Y chromosome being non-recombining, called the NRY (non-recombining region of the Y chromosome). It is easy to track mutations in the NRY, because each mutation is subsequently passed onto all male offspring, creating a permanent history of the mutation (Weidenbach, 2000). These mutations, which are designated into haplogroups then haplotypes, can be used to trace back population migrations and variation. Unlike autosomal DNA, which is inherited from both parents, the NRY shows the ancestral history of a specific male lineage.
Indigenous Native American populations show a predominance of Y chromosome haplogroups Q, R, and C. Geographic regions show variation within those groups through various haplotypes based on differential STR number data (Schurr, 2004, pp. 557). “C, Q, and R accounted for nearly 96% of Native American Y chromosomes. Haplogroups C and Q were deemed to represent early Native American founding Y chromosome lineages; however, most haplotype R lineages present in Native Americans most likely came from recent admixture with Europeans” (Zegura, 2003, pp. 164). Native American NRY diversity is much less than the diversity seen in Asian NRY’s, including a reduction in STR replication haplotypes.
Until recently there was not a unified method of categorizing new Y-chromosome haplotypes found using STR markers leading to identical mutations being labeled differently. Due to this, subdivisions of Q-M3, found in all Native American populations, are clustered...