Effective 21 March 2011, the majority of the clade names in Haplogroup R were updated. We recognize this is a disruption to the user community, and apologize for the inconvenience. The background for the changes is detailed here.

On 5 March 2011, Family Tree DNA (FTDNA) announced a major revision to the Y haplotree which they use for defining haplogroups, as well as determining which SNPs are a part of their standard "deep clade" tests.

Family Tree DNA, in partnership with the YCC, periodically reviews known SNPs in order to evaluate those that meet the requirements to be added to the haplotree. The SNPs that passed this review are now included in the haplotree and considered for deep clade testing.

For most haplogroups, the differences between the current ISOGG 2011 haplotree and the new FTDNA 2011 haplotree were minor and readily resolved. However, for Haplogroup R, there were a number of differences, falling into three general categories.

1. SNPs present on the ISOGG tree that are not included on the FTDNA tree.
FTDNA's cutoff for new SNPs was quite some time ago, due to their lead time requirements for making database and web page modifications, and they did not have the opportunity to incorporate the very latest SNP developments. The new SNPs remain on the ISOGG tree.

2. SNPs present on the FTDNA tree that were not included on the ISOGG tree.
These were primarily "private" SNPs. ISOGG normally does not include SNPs unless there are clearly multiple derived examples found among unrelated people. Typically, this would be three or more people, where there is a minimum of a 15% haplotype variation between them. FTDNA uses a different standard for inclusion, and as a result they included additional private SNPs on their 2011 Haplotree that were not on the ISOGG tree. To reduce the possibility of confusion due to arbitrary differences between the two trees, the additional private SNPs have also been included on the ISOGG 2011 tree in most cases, and are color-coded and marked as private.

3. Ordering of SNPs within the haplotree.
ISOGG normally adds new clades at the end of the list of their peer clades, in order to minimize the disruption to existent clade names. FTDNA and YCC follow the academic practice of listing clades in the order of the discovery of the SNPs. As result, there were significant differences in the order of the SNPs in several areas of the Haplogroup R tree, which caused the clade based haplogroup names to also differ. After careful consideration, ISOGG chose to adopt the ordering used by FTDNA and YCC in order to minimize arbitrary differences that would contribute to confusion in the genetic genealogy community. The expectation is that the next YCC update will also reflect this ordering, and since the YCC tree is widely used by the academic community, conforming to their ordering will help minimize terminology differences between the ISOGG tree and academic papers.

Due to the preponderance of Haplogroup R among peoples of European and SW Asian descent, a disproportionate amount of Haplogroup R research and testing is done. As a result, there are typically more discoveries, and more disruptions, to the structure of the Haplogroup R tree. In particular, clade based haplogroup names (e.g. R1b1b2), which are based on the structure of the haplotree, as well as the ordering of SNPs within the tree, are especially sensitive to change in the Haplogroup R tree. Using mutation based haplogroup names (e.g. R-M269) is preferable in Haplogroup R, as a mutation based name will not be affected by changes in the tree structure or SNP ordering. FTDNA refers to the mutation based name as the "shorthand" name.