mtDNA and Y chromosomes from pre-Columbian Andean Highlanders

They found all A, B, C, D mtDNA haplogroups. The evidence for genetic continuity can probably be ascribed to the small timespan to the present, and the relative isolation of Amerindians in comparison to populations of Eurasia where genetic discontinuities have been discovered over longer time periods.

From the paper:

All individuals belong to haplogroup Q1a3a∗. Only individuals where it was possible to determine the full profile of six SNPs are considered here. There is a high number of individuals showing allelic dropout, presumably due to DNA degradation, for one or more SNPs. For two individuals with realised polymorphisms in M242 and M3, only M19 could not be typed, so there is a chance that these individuals could belong to haplogroup Q1a3a2 and not Q1a3a∗.

Annals of Human Genetics doi: 10.1111/j.1469-1809.2010.00620.x

Diachronic Investigations of Mitochondrial and Y-Chromosomal Genetic Markers in Pre-Columbian Andean Highlanders from South Peru

Lars Fehren-Schmitz et al.

This study examines the reciprocal effects of cultural evolution, and population dynamics in pre-Columbian southernPeru by the analysis of DNA from pre-Columbian populations that lived in the fringe area between the Andean highlandsand the Pacific coast. The main objective is to reveal whether the transition from the Middle Horizon (MH: 650–1000 AD) to the Late Intermediate Period (LIP: 1000–1400 AD) was accompanied or influenced by population dynamic processes. Tooth samples from 90 individuals from several archaeological sites, dating to the MH and LIP, in the researcharea were collected to analyse mitochodrial, and Y-chromosomal genetic markers. Coding region polymorphisms weresuccessfully analysed and replicated for 72 individuals, as were control region sequences for 65 individuals and Ychromosomalsingle nucleotide polymorphisms (SNPs) for 19 individuals, and these were compared to a large set ofancient and modern indigenous South American populations. The diachronic comparison of the upper valley samples from both time periods reveals no genetic discontinuities accompanying the cultural dynamic processes. A high genetic affinity for other ancient and modern highland populations can be observed, suggesting genetic continuity in the Andean highlands at the latest from the MH. A significant matrilineal differentiation to ancient Peruvian coastal populations can be observed suggesting a differential population history.

Link