Listing Criteria for SNP Inclusion
into the ISOGG
Y-DNA Haplogroup Tree - 2013
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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.
- 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.
- STR Diversity or BP Frequency
To be accepted the BP must be observed in at least two individuals, and
must meet either the minimum BP frequency requirement OR the STR diversity requirement. A BP
that does not meet either requirement will be classified as a Private SNP (see section 12).
Note that there is no requirement that the individuals have unique surnames.
a. The minimum BP frequency requirement is met if a specified population is 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.
b. The SNP diversity requirement is met if the following conditions are satisfied:
i. If the BP is a Non-Terminal Branch BP (see section 6), the diversity requirement is met de facto,
and no further proof of diversity is required.
ii. Genetic distance is calculated using the Infinite Alleles Model.
iii. All markers tested by both individuals must be compared.
iv. If 74 markers (or fewer) are compared, the minimum genetic distance to meet the diversity
requirement is 7.
v. If 75 (or more) markers are compared, the diversity requirement is a minimum of 10%, computed
by dividing the genetic distance by the number of markers compared, and rounding to the nearest integer value.
- 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. In addition, one person in each of Haplogroups I, J, and K
must be shown to be ancestral for the new BP.
- 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 one individual who is derived for the new BP is tested
for every existing sub-branch (i.e. brother clade) defining BP, with the exception of
private BPs (see section 12), and shown to be ancestral for these brother clade
- at least one individual who is derived for each brother clade BP is
tested for new BP and shown to be ancestral for the new BP.
- In the case where the new BP is a new terminal sub-branch of an existing terminal
BP, then it must be demonstrated that it is not restricted solely to close
relatives by meeting the requirements outlined in section 5. STR Diversity or BR Frequency.
- 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
Alice Fairhurst and
describe where the new BP fits in the cladogram. Alice will forward the information to the appropriate
haplogroup experts for evaluation for inclusion on the tree. 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 a BTP that
did not meet either the frequency or diversity requirements outlined in Section 5. In most cases,
a BP will be listed initially as a SNP Under Investigation and will
be moved to the Private designation after sufficient testing has been done.
- SNPs under Investigation are BPs that have not yet been placed on the tree
because additional testing is needed to confirm adequate positive samples and/or correct placement on the tree.
Corrections/Additions made since 1 January 2013:
- Under Non-Terminal Branch, remark 6b has been modified on 10 February 2013.
- The old 3. paragraph has been removed; paragraphs 4 and 5 have been moved to 3 and 4 and a
new 5. paragraphy on STR Diversity or BP Frequency has been inserted on 23 May 2013.
- Under 6, b. has been revised; under 7 all paragraphs have been revised; 12 has been revised on 23 May 2013.