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From:
Subject: Re: [DNA] good article on Y chromo
Date: Mon, 2 Sep 2002 09:50:54 EDT


In a message dated 09/01/02 8:09:08 PM Pacific Daylight Time,
writes:


> http://www.ukpoliticsmisc.org.uk/usenet_evidence/gene_legacy/
> The Genetic Legacy of Paleolithic Homo sapiens sapiens in Extant Europeans:
> A Y Chromosome Perspective

Interesting that you found the article on the above web site! It was
published in Science magazine, so for a complete citation and other helpful
links, see the original source at

http://www.sciencemag.org/cgi/content/full/290/5494/1155

Some have asked about how the terminology in this article (haplogroups)
relates to results from genealogical testing (haplotypes). I've tried to
explain this many times in many different ways, but I guess I'm not getting
though, so maybe somebody else could take a stab at it. Sometimes a different
turn of phrase will help, but I'll say this one more time, and then stop
writing on the topic, because I fear that people get too hung up on the
concept of haplogroups.

Basically (in the context of Y chromosomes), haplogroups are defined by
slowly changing markers (with names like M170 and YAP). These markers are
sometimes called biallelic or binary markers, because they come in two
flavors, where the mutation is either present or absent. They are also called
UEPs (Unique Event Polymorphisms), because it is believed that the mutation
occurred only one time in all of human history.

Haplotypes use an entirely different method with more rapidly changing
markers, the STRs (short tandem repeats, many of them labeled with DYS
numbers). These markers also have an advantage that they have many alleles
(variations, in this case, changes in the number of repeats).

The population geneticists focus on haplogroups, because they are interested
in broad migration patterns of early man. Genealogists focus on haplotypes,
because they are interested in recent history. If you run both kinds of tests
on a group of people, you will find that each haplogroup has a wide variety
of haplotypes. Each haplogroup will have a modal haplotype (the single most
common haplotype), but we can't always go from the haplotype to the
haplogroup. They are different tests.

Semino's paper was written before the Y Chromosome Consortium published a
proposal for standardizing nomenclature. See Figure 1 for a table which lists
the markers and the terminology used by different researchers. I keep the PDF
file on hand to zoom in, because the printout is fuzzy.

http://ycc.biosci.arizona.edu/nomenclature_system/frontpage.html

Ann Turner
GENEALOGY-DNA List Administrator
http://lists.rootsweb.com/index/other/Miscellaneous/GENEALOGY-DNA.html
DNA preservation kits: http://www.dnafiler.com

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