Wednesday, February 25, 2009

X and Autosomal DNA

I want to quote here a posting to the DNA List made by Kathy Johns which, although I'm not sure I completely understand it, seems to me to help begin an understanding of what we might expect from the developing and maturing field of X and Autosomal DNA.
First of all, it is kind of Tim to call us pioneers but the truth of the matter is that we may think we are pioneers, but those of us who are in the X chromosome study group are actually rediscovering (for the first time for us) information that was already out there but not widely known or understood.

To address your concern about the methodology. We should not be applying percentage ancestral origins to the definition of haploblocks at all.    The percentage ancestral origin just gives us your best guess as to the probability of each ethnic or geographic origin that contributed to your X as a whole, nothing more than that.    We are also not including the ends of the chromosome where there is a lot of crossover recombination.

The main reason for asking people to calculate their percentage of X ancestry is to determine where your X might have come from.    It makes no sense to give us your percentages from a man's father, for example because your father would contribute nothing to your X if you are a male - neither would your mother's father's father's line.    It helps to know that your mother's father's mother's father's line contributes a whole lot more to your X (on the average) than your mother's mother's mother's mother's line etc.    Knowing the probabilities and the geographical areas could eventually lead to the identification of some ancestors that carried a particular mutation in a particular block, or hopefully give us a set of STRs or other hypervariable regions within a block that could be used to identify founders.    We are talking about origins here within a genealogical time frame.    Each of our X chromosomes is a mosaic of several blocks of founders spliced together, not just one as in the Y chromosome.    We expect to find some of the same types of haplogroups.

Some people have found what they think might be SNPs representing a particular ethnic group, or a founder effect but we are not ready to attach assignments yet.    Some blocks just look promising because the pedigree seems to have an ancestor from a distinct geographical area and we think we might be seeing identifiable founder sequences in that same chromosome.    It is really too early to tell.

Sometimes a particular block is assigned an origin based on the fact that deCODEme has reported the block's ancestry painting to be of a certain race, for example, African, but that is really a misnomer.    I have also used the term "African" when nearly 100% of Sub Saharan Africans in HapMap have had a particular SNP sequence.    But as we have also discovered, those of us who have detected these sequences in ourselves at 23andMe really don't have African in the recent past.    These blocks just happen to be older than our species in some cases but also match some African populations.    These same blocks have at the other end of the spectrum, an "Asian" block that matches none of the Sub Saharan Africans.    Most Europeans will fit into one or the other and can have both depending on the rate of recombination in these ancient blocks.    Other blocks seem to have much more variation.    Some blocks will probably never be classifiable.

Thank you, Kathy.


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