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Archiver > AUTOSOMAL-DNA > 2014-04 > 1396634930


From: Jim Bartlett <>
Subject: Re: [AUTOSOMAL-DNA] The significance of segment overlaps
Date: Fri, 04 Apr 2014 14:08:50 -0400
References: <6420670.2501550.1396584058103.JavaMail.root@vznit170158><885498EC-D0D1-47A8-AC82-34F107C8B01B@ucla.edu>
In-Reply-To: <885498EC-D0D1-47A8-AC82-34F107C8B01B@ucla.edu>


Don

I, too, have contemplated the "march" of overlapping segments in a TG. I rationalize it this way: the Common Ancestor of the TG started with a full chromosome, and passed down large segments to the children, who passed down segments of various sizes to further descendants on down to the Matches in a TG. The segment I got from that CA is almost always larger than the shared segment with each Match - each Match having gotten their own segment from the CA. A Match could get a segment from a CA that extends father than mine on one end of mine, or the Match may have a smaller shared segment with me within the segment I got. A Match that matches me and the TG "exactly", probably got a larger segment than I did - my segment could be totally within the Match's segment. In fact each of the Matches in my TG, would probably have a different TG of their own, with their Matches - maybe even some that were outside the range of matching me. This highlights the concept that it's important t!
o remember the base person (usually ourselves) when making comparisons.

In the full map of my chromosome from one parent, I try to look at the adjacent segments, to keep things in perspective. TG-segments on one chromosome (from a specific ancestor) should not overlap. I find that the various segments on a chromosome, when they can be assigned to a parent (usually as a TG), have pretty well defined break points, even gaps, between segments. Of course unassigned segments (to a side/parent or TG) can overlap the TG segments and create confusion - it's important to "look through" those segments and just focus on the TGs.

Each of my "ancestor" segments, is becoming pretty well defined, and new Match-segments fit in nicely, and add another potential researcher to the TG. And still, it's hard to agree on an MRCA.

I've also encountered a number of TGs with overlapping ends or "tips" - usually within 1Mbp of overlap. I generally think this just reflects the fuzzy nature of segment ends - this reinforces that concept.

Without 2-parent phasing, and a detailed examination of the ACGTs, I may never know the precise location of the crossover points (between one ancestor and another). But then, that is not critical to my objectives - I want to link different ancestors to different segments and try to account for most of my genome. I want a Kitty Cooper map that fills in most of the picture with the shortest segments possible (7cM is my current threshold)

I think this process will be one of repeated refinements. At the end of the day, we should be able to show the few large segments from our grandparents that cover each chromosome; and then how those segments are subdivided, usually into two parts by the appropriate G or 2G or even 3G grandparents; and then those medium sized segments are further split by even deeper ancestors; until the next split results in a segment below the matching threshold. Then, and only then, I'll look to GEDmatch for smaller shared segments...

Back to my spreadsheet;>j

Jim - Sent from my iPhone - FaceTime!

> On Apr 4, 2014, at 12:39 AM, Don Worth <> wrote:
>
> Thanks, Jim. It seems like we are pretty much in agreement.
>
> One interesting comment you made was that your TGs can contain two segments that do not overlap at all - the first segment(s) in a TG and the last one(s). I see this all the time in my ADSA outputs. The segments "march" across the page from left to right and by the time the later ones start the early ones have ended (if they are short) or, at least, they don't overlap the early ones by much at all. This, of course, affects the ICW outcomes since the early ones don't (necessarily) ICW the later ones. In ADSA the rectangular block of little colored bricks kind of "flakes" away at the upper left corner and the lower right corner so that it's not a perfect rectangle of ICWs.
>
> It feels a little "transitive" to presume that the early ones and the later ones are part of the same ancestor's segment. I guess I could go either way on that. I worry about two very different ancestral-segments lying side by side abutting each other with little match-segments spread out across them like overlapping shingles. If even one segment in the middle doesn't overlap the next (or has fuzzy boundaries) this scenario seems possible.
>
> Don


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