Listing Criteria for SNP Inclusion
into the ISOGG
Y-DNA Haplogroup Tree - 2008
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- These recommendations are to assure that there is a uniform set of criteria for
accepting binary polymorphisms for defining and placing clades on the ISOGG Y-Chromosome
Haplogroup Tree. We define binary polymorphism (BP) as a polymorphism with two states.
It could be a single nucleotide polymorphism (SNP) or an insertion/deletion (indel).
- While not a part of the definition for binary polymorphism, it is expected that the
markers proposed for inclusion as defining markers for haplogroups will also have the
characteristics: (a) the effective mutation rate will be less than approximately 5 x 10-7,
and (b) that the polymorphism has not been observed more than twice in human history.
- To be accepted the BP has to be observed at least twice in separate individuals and
satisfy either the frequency or STR diversity requirements to exclude the BP from being
classified as private (as defined in section 12).
- In exceptional cases other variants may be considered for inclusion on a case by case
basis if they can be clearly demonstrated to have an allele state or range with equivalent
properties to binary markers, but the burden of proof required will be much higher and at
the discretion of the committee.
- We would like to avoid the inclusion of new binary polymorphisms where it is not clear
how they relate to previously established binary polymorphisms.
- Non-Terminal Branch BPs
- The supporting information provided by the proposer should demonstrate that the new
BP is downstream of an established BP and has been tested in individuals who have also
been tested for all potential (well established and non-private) downstream BPs.
- For example, suppose that a new BP is discovered and that it is claimed to be 1)
within Haplogroup F and 2) ancestral to both Haplogroups G and H, but not to I, J, or K.
Then several persons should have been tested to demonstrate that those who are confirmed
as being in either Haplogroup G or Haplogroup H are also derived for the new BP, and that
at least two persons who are in each of Haplogroups I, J, and K are ancestral for the new
BP. The individuals tested in each group also need to be unrelated. The test for
unrelatedness here and elsewhere will be the provision of an associated STR haplotype whose
allele values differ in 15% or more of the markers genotyped.
- Terminal Branch BPs
- In the case where the new BP is the terminal branch of an existing clade that already
has existing sub-branches, then:
- at least 2 unrelated individuals that are derived for the new BP need to be tested
for every existing sub-branch (i.e. sister clade) defining BP, with the exception of
private BPs (see section 12), and shown to be ancestral for these sister clade
- at least 2 unrelated individuals that are derived for each sister clade BP are
tested with the new BP and shown to be ancestral.
- In the case where the new BP is the new terminal sub-branch of an existing terminal
BP, then it should also be demonstrated that it is not restricted solely to close
relatives. This can be achieved by demonstrating that two or more derived state
individuals have greater than 15% mismatches in their associated STR profiles, plus any
results where the ancestral state of the BP was detected.
- Acceptance Process
- The ISOGG committee will accept proposed new BPs in a two-step process. First the
discoverer of the BP (or a third party, knowledgeable about the BP) can email
Whit Athey or
David Wilson and
describe where the new BP fits in the cladogram. The committee can tentatively incorporate
this BP according to this advice and make any structural changes to the haplgroup tree
necessitated by it. The discoverer (or third party) then would provide the evidence as
stated above for the proposed placement within the period of one month from the provisional
placement on the tree. Therefore, new BPs should not be submitted until this deadline is a
reasonable one. When the additional information is received, the BP would be classified
as either added (full confirmation) if full evidence as
described above was available, or confirmed (within subclade)
if sufficient information was available to meet that requirement (see below). In the latter
case it would be expected that when sufficient additional evidence was collected it would
be provided and the BP would move to added (full confirmation).
- Added BPs are color coded and defined as: BPs that
have met all of the criteria listed above for inclusion and did not appear on last year's tree.
- Provisional BPs are color coded and defined as: BPs
newly submitted to the ISOGG committee that have sufficient information to be placed in the
tree with some certainty, but insufficient to meet all the criteria above and are
awaiting evidence as described above.
- Confirmed BPs within Subclade are color coded and defined as:
a BP that has been demonstrated through use of an appropriate logic model and testing that the
BP is within the subclade shown on the tree. This classification is appropriate where derived
samples for some or all of the other BPs within the same subclade are not yet available for testing.
- Private SNPs are color coded and are defined as:
- EITHER a BP that has been observed only once, or has been observed multiple
times but the associated STR profiles show less than 15% of markers have diverged.
- OR a BP for which NO specified population have been demonstrated to exist where
the frequency is greater than 0.05% (P<0.05) and whose total male population exceeds 500
thousand individuals as defined geographically or ethnically.
Corrections/Additions made since 31 December 2007:
- Reclarified points 9, 10 and 11 on 4 May 2008.
- Changed contact person from John McEwan to David Wilson on 23 October 2008.