We have just considered recLOH events in which the multi-copy markers on a palindromic arm can all change significantly and only result in a genetic distance of one. Pending authoritative directions otherwise I have determined how I will advise the members of this surname project to count genetic distances for differences in multi-copy markers that are not part of a recLOH event. Multi-copy markers are those markers that have a small letter of the alphabet associated with them, i.e., DYS385a & b, DYS459a & b, DYS464a,b,c & d, CDYa & b, and YCAiia & b.
Consider that each of these markers is made up of two or more 'parts', each part represented by a value, e.g., DYS385a is 11 and DYS385b is 14, so we will designate DYS385 as 11-14, the two 'parts' being 11 and 14. If either part changed to another value, no matter what value, it would be a mismatch of one 'part' and therefore a distance of one. So 11-15 would be a distance of one from our example. 11-17 or 13-14 would likewise each be a change of one part from 11-14 and a distance of one. 12-13 or 13-15, however, would each be a mismatch of both (2) parts and a distance of two. This illustration will apply to any of the two part markers.
The other case is DYS464 which is a four (or more) part marker. The numbers for it are reported in lowest to highest format which is not necessarily their actual order. So for DYS464 we have to determine how many markers the two people do not have in common. Assume DYS464 is 14-14-16-18. We want to know the genetic distance of 14-16-18-18. Both have a 14, 16 and 18 in the series -- although not in the same positions -- position doesn't matter on this marker. So 3 of the 4 numbers are the same, a 1 step mismatch, ergo a distance of one. 12-14-15-16, on the other hand, only has two markers in common, 14 and 16, so we have a two part mismatch or a distance of two.
Come to think of it, I have never seen the values of any multi-part markers reported in anything other than low to high format, no matter how many values. That being the case I'll go out on a limb just a little and suggest that if we have a two part marker like CDY as 35-39 and we want to compare another marker of 39-40 with it, the distance should be one since we have a mismatch of only one value.
In summary, if it's a recLOH event it's a distance of 1 for the whole event (all multi-copy markers on a given palindromic arm) and if it's not a recLOH event just count each multi-copy marker as a unit, not each part of the marker. Compare the parts but count the marker.