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Measuring Haplotype Rarity

Implications of Commonness vs. Rarity

To restate the, perhaps, obvious:
We take the purpose for Y-STR testing to be the identification of shared Y-chromosomal inheritances by means of haplotype similarities. If similarities are due to factors other than inheritance from a shared direct paternal ancestor, they are misleading and the purpose is not attained.

An implication of common haplotypes is that they are similar to each other. In order to properly identify patrilines, those with more common haplotypes need higher resolution[7] levels and perhaps more SNP testing than those with uncommon or rare haplotypes. Conversely, those with rare haplotypes may achieve the same goal with less testing.

Other implications affect grouping into paternal genetic families. Members of the same genetic family should have similar (though not necessarily identical) scores on any commonness/rarity measure.

And, apparent matches between those with common haplotypes may be more likely to be coincidental rather than reflect shared patrilines[8].


We believe this study implies the following to Y-STR testers and project administrators

  1. Men with very common to average haplotypes (the 75% lowest scoring on the metrics) need to test more markers (higher resolution) in order to differentiate a patriline.
    1. Matches at low resolutions are likely to be coincidental.
    2. Average (50% middle scoring) haplotypes may more likely differentiate patrilines at a resolution of 37 markers.
    3. Common haplotypes may differentiate  at 67
    4. Very common haplotypes may require 111 markers or more to differentiate.
  2. Men with uncommon to rare haplotypes may test to lower resolutions
    1. Some patrilines may be identifiable by "signature" values only only a few markers, occurring early in the marker sets.

Unfortunately, the commonness of a man's Y-haplotype can be determined only after at least some markers are tested and successively upgrading resolutions is an expensive and cumbersome process.


The extreme example of the common haplotype is the WAMH. A strictly statistical concept it is in no way to shared patrilines within a genealogical time frame. Men exactly matching WAMH do not necessarily share a common direct paternal ancestor within many millennia. Therefore, a project admin would be remiss to conclude that all WAMH men belong to a single Y-genetic family.

There are other other haplotypes almost as common as WAMH. (Most haven't received special labels.) For them too grouping into a single genetic family would be misleading as to shared patrilines.

Rules of Thumb

Many admins use rules of thumb (for example, steps of genetic distance) to simplify the grouping task. But grouping is not a task for one rule fits all. These rules need to be adjusted to the rarity status of the haplotype. A rare haplotype may permit a looser rule to be applied, while a common haplotype requires a stricter rule.


Men with more common haplotypes may be more likely to have high numbers of "close matches", many of which are meaningless in terms of shared patrilines.

However, men with rarer haplotypes may have find close matches at all wihtin the FTDNA database.