The History and Geography of the Y Chromosome SNPs in Europe: an update
2010
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.
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