Haplogroups
From SNPedia
Ancestry
Haplogroups mark the migration from common ancestors to distinct regional populations.
Haplogroup Y (Y-DNA) is the root of the Y Chromosome Haplogroup Tree.
This blog summary of the human genographic project from national geographic is well written.
The paper [PMID 18385274] is currently the best reference for the Y chromosome. The supplemental material is available at [1] and is sufficient for determining a reasonable collection of snps for the criteria of a genoset which recognizes a haplogroup. [2] provides a nice poster although it lacks the mapping to rs#.
The Y-chromosome has a lower SNP mutation rate than mtDNA.
There was a recomendation from the Y-chromosome consortium, YCC, to change to a short hand. That is to write R-P312 rather than R1b1b2a1a2.
ISOGG Tree version is 2010 http://www.isogg.org/tree/index.html
ISOGG List of SNP markers for Haplogroups http://isogg.org/tree/ISOGG_YDNA_SNP_Index.html
YCC table of markers with ancestral/descendant changes (but old and incomplete) http://ycc.biosci.arizona.edu/nomenclature_system/data.html
current version of the YCC tree. http://www.familytreedna.com/snps-r-us.aspx
The STR predictions are handled by Whit Athey's tool. http://www.hprg.com/hapest5/
ySearch ID pages are the easy way to read in STR data. For example: http://www.ysearch.org/haplosearch_view.asp?viewuid=FB88E
This GoPubMed search for Haplogroups might be of some use
