The History and Geography of the Y Chromosome SNPs in Europe: an update

The knowledge of the evolution of the human genome is strictly dependent on the availability of appropriate genetic markers and their relative coverage of genetic variation which refine the phylogenetic reconstruction. While autosomal markers are particularly valuable for recognizing correspondence between genetic and geographic distances, markers on mitochondrial DNA (mtDNA) or Non Recombining Portion of Y Chromosome (NRY), because of their unilinear transmission, can effectively trace diachronical patterns of the human peopling. The maximum extent of polymorphism coverage has already been reached for the very small mitochondrial genome (about 16,5 Kbp), whereas the first studies based on RFLPs (Restriction Fragment Length Polymorphisms) (Cann et al. , 1987) and on sequencing of the hypervariable regions (Vigliant et al. , 1991), were then combined to get higher resolution (Torroni et al. , 1996), and finally the complete genome sequencing is now routinely performed (Achilli et al. , 2004, Pala et al. , 2009), in order to detect the whole mtDNA variation. A similar approach cannot be used yet at population level for the by far larger nuclear genome. However, advances in genotyping technology have dramatically enhanced the resolution of the analysis at genome-wide level, and recent papers significantly improved the knowledge of the relationships among European populations, using 300 to 500 K SNPs (Single Nucleotide Polymorphisms) on microarrays chips (Tian et al. , 2008; Novembre et al. , 2008). As to the NRY, most of the studies before the year 2000 were performed using Alu insertion (Hammer, 1995) or STRs (Short Tandem Repeats) (De Knijff et al. , 1997; Pritchard et al. , 1999) with the known limitations due to recurrence and reversion of this kind of polymorphisms. Using D-HPLC (Denaturing High Performance Liquid Chromatography) technology, Underhill and coworkers (1997) discovered 22 new SNP biallelic markers, rapidly raising in number to 167 (Underhill et al. , 2000), 242 (YCC, 2002), about 600 (Karafet et al., 2008), up to more than 725 presently listed in the Y-DNA SNP Index 2009, (www.isogg. org), and the knowledge of Y chromosome phylogeny and of the spread worldwide of human populations raised proportionally. The next goal of the research on Y chromosome will be the use of specific microarrays that can genotype a much higher number of SNPs than nowadays routinely performed, and, ultimately, the complete Y chromosome sequencing. Waiting for future developments, this short note reports the state of the art of the phylogenetic (“history”) and phylogeographic (“geography”) research on Y chromosome SNP analyses in Europe, updating the review published in this Journal by Francalacci & Sanna at the beginning of 2008.