MALDI-TOF MS analysis of Y-SNPs in ancient samples

Abstract

Studying ancient central Asian, Siberian and South American populations with classical markers (nuclear microsatellites and mitochondrial DNA sequence polymorphisms) allowed us to investigate parental relationships among individuals from burial sites revealing funeral practices. Ancient DNA studies can also provide information on the origins and the history of population from the past. Focussing on biallelic markers which have a lower mutation rate than repeat polymorphism, it is possible to address events corresponding to longer periods of time. In the frame of our anthropological studies on ancient DNA samples from Mongolia, Siberia, Yakutia and South America, we concentrated efforts on three Y chromosomal SNPs (TAT, M242 and RPS4Y) known to have specific allelic distributions in these populations or to be informative regarding the peopling of America (M242 and RPS4Y). Facing ancient samples where DNA is strongly degraded and scarce requires the use of technologies which can provide information from only short fragments of intact template. In this context, we developed a primer extension and matrix-assisted laser desorption ionization time-of-flight mass spectrometry-based multiplexed reaction for the investigation of these three polymorphisms. The tested ancient male specimens were recovered from a necropolis located south of Lake Baïkal in northern Mongolia (Egyin Gol valley). Distinct SNP profiles were obtained enlightening the ethnic heterogeneity of the Xiongnu tribe which was only foreshadowed by the STR marker analysis.