Genetic variation of maternal and paternal lineages within the Havasupai Indians of northern Arizona

Abstract

The Havasupai Indians are a small (∼600 members), Yuman-speaking population that resides on a reservation in the Grand Canyon region of northern Arizona. Due to their location and cultural practices, they are subjected to extreme geographic and reproductive isolation. Additionally, an influenza epidemic at the turn of the century decreased the reproducing population to 43 females and 42 males. These observations suggest that the Havasupai should contain less genetic diversity than other Native American populations. They are also disproportionately affected by disease, having the third largest incidence of Non Insulin-Dependent Diabetes Mellitus (NIDDM) in the world. An extensive analysis of maternal and paternal variation of the Havasupai was undertaken. Maternal variation was assayed by sequencing the non-coding control region (CR) of mitochondrial DNA (mtDNA), whereas paternal variation was examined using single nucleotide polymorphisms (SNPs) and short tandem repeats (STRs) located on the non-recombining portion of the Y-chromosome (NRY). Due to the availability of familial pedigrees dating back to the mid-1800s and spanning eight generations, precise mutation rates were determined for maternal and paternal lineages. The Havasupai thus offer a unique opportunity to explore genetic variation in a small, homogenous Native American population for which extensive genealogical information is readily available. Examination of mtDNA sequences from the complete 1127 by CR of 43 Havasupai individuals along with SNP and STR data from the Y-chromosome of 48 male Havasupai revealed that contrary to our initial prediction, the Havasupai, historically a small population (as evidenced by the limited number of founder haplotypes and low estimates of π), probably maintained a relatively high level of diversity (as evidenced by the number of rare haplotypes, high haplotype diversity, and high estimate of E(ν)), probably a remnant of their association with the larger Pai population from which they are derived. As the level of diversity displayed by the Havasupai seems to have been maintained since the recent population bottleneck, it must have been too small and/or too short to have any detectable effect on the overall diversity of the tribe. Lastly, there appears to be some association between mtDNA mutations and NIDDM in the Havasupai population.