Last week I reported that it turns out that one of my siblings carry a possible Neandertal haplotype on the dystrophin gene. To review, it seems likely that ~3% of the average non-African's genome is derived from Neandertal populations. But by and large this ancestral quantum seems broadly dispersed through the genome of individuals, so that there isn't a particular set of loci which are Neandertal, as such. As an analogy, about ~20-25% of the genome of an average black American is derived from Europe because of white American ancestry. But you can't usually predict from that on which locus the "white" alleles will be found. The main exception to this will be loci where you might suspect selection will be operative, such as those implicated in malaria defense (some of them have negative consequences).
The dystrophin haplotype though has higher frequencies in some populations than expectation. ~9% in non-Africans as a whole, and higher in some groups. So there was a reasonable expectation that people might find that they carried it snooping through their genomes. Now that my parents (RF and RM) have come through, as well as sibling #2 (RS2), I can show you this:
SNPs
rs1456740rs6628685rs331370rs2854965rs6653863rs331369rs331368rs331367rs331366
RFAATGAATTT
RS1A/GA/AC/TG/GA/GA/CT/TT/TG/T
RazibGACG(not typed)CTTG
RMA/GA/AC/TG/GA/GA/CT/TT/TG/T
RS2AA(no call)GAATTT
As you can see RS2 and RF have a single copy of the Neandertal haplotype. That's because males only have one X chromosome. In contrast, females have two, so you can't know immediately what the haplotype necessarily is just by looking at the sequence of genotypes which you can extract out of the 23andMe browser. But since males inherit the X chromosome from their mother, one can infer that my mother is a heterozygote for the Neandertal haplotype, B006, and B001, the most common Eurasian one. So here's what I can figure out:
SNPs
rs1456740rs6628685rs331370rs2854965rs6653863rs331369rs331368rs331367rs331366
RFAATGAATTT
RS1AATGAATTT
GACGGCTTG
RazibGACG(not typed)CTTG
RMAATGAATTT
GACGGCTTG
RS2AA(no call)GAATTT
Obviously I don't know if there's any functional significance which correlates with these markers. But note that on this particular locus I'm 0% Neandertal, while RS2 is 100% Neandertal, while RS1 and RM are 50% Neandertal. Though I doubt that the quantum of total Neandertal admixture differs at all within the family, there's going to be variance at any given locus (though on most loci presumably the alleles will be descended from neo-Africans across the family).
Note: for the record, I am moderately disappointed that I didn't win the Neandertal genetic lottery on this locus.
