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From: "Ken Nordtvedt" <>
Subject: Missing Links
Date: Sat, 1 Apr 2006 12:34:09 -0700


I could not help but notice in a recent message to the list which asserted that we dare not assume genetic continuity from the present back to paleolithic times --- because we can only measure y-haplotypes of today, and because there are some claims that ancient measured mtDNA haplotypes are showing discontinuity with the present --- there was also a claim that arrival of J into Europe with the spread of agriculture had a slam-dunk (but nevertheless inferred) connection? J ydna haplotypes are also known only as we see them today; so I don't buy the double standard being deployed here?

We have an ever-growing array of new tools today that were not used in some of these older papers. So measurements are possible which can produce data relevant to questions earlier addressed with perhaps too much speculation or extrapolation.

The SNP S22 which establishes the "missing link" population of IJx(I,J) is one such new tool. Certainly southeast Europe and the Mideast ought to be scoured for examples of IJ haplotypes. It is even worthwhile hunting for some IJx(I,J) haplotypes in our most-used databases --- Ysearch and SMGF --- but due to their biases toward NW Europe, dedicated searches in the SE of Europe and Mideast probably have more promise of discovery. Actually we don't even know what an IJx(I,J) extended haplotype looks like, or whether they still exist, or if exist in what percentage and where?

Similarly, if we want to learn something about the early times of haplogroup I, we now have more tools to find the populations of I* and I1*. I am especially speaking of SNPs P38 and S31 which sit between the founding of haplogroup I and the robust populations I1a (P30+), old I1b (P37.2+), old I1c(M223+), newly found "old I1(x)" and "old I1(y)". See www.northwestanalysis.net for I Tree and new names for these old sub-clades as well as placements of the new and old SNPs.

There are no known examples of I* or I1* haplotypes except for two rumored haplotypes in a university collection (reportedly from Greece and Israel). We have the tools to look for these clades in NW Europe, but better to look from Mediterranean lands and SE Europe. One unpublished study isolated about 150 haplogroup I haplotypes with M170+. Every one of these haplotypes was later found to comfortably fit in one of the downstream clades of I mentioned above, either by further SNP results or by extended haplotype structure. There was not one candidate haplotype for I* or I1*. But the Mediterranean and SE Europe were not sampled. Rootsi et al paper of 2004, which better covered SE Europe and Mediterranean, isolated several hundred I haplotypes with SNP tests. They did not use P38 and S31 had not been discovered yet. So they could not isolate the robust clade "old I1(x)" or the smaller clade "old I1(y)" The 21 haplotypes they classified as I*, really Ix(I1a, I1b, I1c) i!
n retrospect are most likely old I1(x) or I1(y), but there is room here for evidence of some bonified I* or I1* haplotypes within the modern I Tree.

Understanding the "early days" of haplogroups like I require deliberately looking for the missing link haplotypes. If you have an I haplotype which as defied classification within the established I sub-clades --- either by the strange nature of its extended haplotype, or by negative SNP results for the standard SNPs --- P37.2, M223, P30, etc. ---- I encourage you to have some of the next upstream SNPs measured. They are available at Ethnoancestry. Depending on your particulars, this would mean such SNPs as P38, S31, S23. If you have been diagnosed as F but not G, H, or I, then consideration of the IJ SNP, S22, is in order

Ken

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