The Unz Review - Mobile
A Collection of Interesting, Important, and Controversial Perspectives Largely Excluded from the American Mainstream Media
Email This Page to Someone

 Remember My Information



=>
Authors Filter?
Razib Khan
Nothing found
 TeasersGene Expression Blog
/
Neandertal genes

Bookmark Toggle AllToCAdd to LibraryRemove from Library • BShow CommentNext New CommentNext New Reply
🔊 Listen RSS

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
rs1456740 rs6628685 rs331370 rs2854965 rs6653863 rs331369 rs331368 rs331367 rs331366
RF A A T G A A T T T
RS1 A/G A/A C/T G/G A/G A/C T/T T/T G/T
Razib G A C G (not typed) C T T G
RM A/G A/A C/T G/G A/G A/C T/T T/T G/T
RS2 A A (no call) G A A T T T

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
rs1456740 rs6628685 rs331370 rs2854965 rs6653863 rs331369 rs331368 rs331367 rs331366
RF A A T G A A T T T
RS1 A A T G A A T T T

G A C G G C T T G
Razib G A C G (not typed) C T T G
RM A A T G A A T T T
G A C G G C T T G
RS2 A A (no call) G A A T T T

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.

(Republished from Discover/GNXP by permission of author or representative)
 
🔊 Listen RSS

There is pretty much a 100% probability that I carry Neandertal origin genes, since I’m Eurasian. That being said, I hadn’t looked too closely into the matter in regards to my own genome, because the whole “which SNPs are Neandertal” issue has been pretty dicey. But after the “Neandertal dystrophin” paper sniffing for whether you carry a specific Neandertal haplotype got a whole lot easier. The authors provided the markers and their associated haplotypes within the paper. So if the B006 haplotye is Neandertal, by looking at your markers in 23andMe through the browse raw data feature you can figure out what your lineage is, and see if you are indeed “Neandertal” on that locus. Since it’s on the X chromosome, males will carry only one copy of the gene. On the other hand, if you’re a woman you’ll have two copies, so ascertaining what specific combination of markers you have spanning a particular genomic segment can be more difficult (the results are not “phased,” so you don’t know if the allele is from the mother or father on any given genotype). But inferring the sequence of markers on a strand of DNA is much easier if you have relatives to compare with.

As you know the results for my first sibling came back earlier this week. I decided to look at which haplotypes we carried. Below the fold are the SNPs (the links will take you to 23andMe, so if you are logged into your account it will take you to where you need to go):


Here the SNPs in the 23andMe data base (one will be missing for v2) :

rs1456740
rs6628685
rs331370
rs2854965
rs6653863
rs331369
rs331368
rs331367
rs331366

Record the genotype. I found it convenient to enter them into a spread sheet if there were two copies for an individual, since you’ll have to engage in elimination of possibilities by looking at the possible combinations.

Here are alleles:

B006 AATGAATTT – Archaic or Neanderthal
B012 AATGAATTT African ancient branch
B007 AATGAATCT African ancient branch
B001 GACGGCTTG World wide distribution
B002 AGTGAATTT World wide distribution
B005 GATTGACCT World wide distribution
B008 GACGGATCT World wide distribution
B009 GACTGCTCG World wide distribution
B003 GACTGCTTG World wide distribution
B010 GATGAATCG World wide distribution
B011 GATTGCCCG World wide distribution
B004 GGTGAATTT Non-African

And now percentages outside Africa rounded to the nearest digit (so if you are female and not African you can eliminate the Africa distinctive possibilities):


Haplotype % outside of Africa
B007 0
B010 0
B012 0
B009 0
B011 2
B008 4
B004 5
B005 5
B006 9
B002 13
B003 16
B001 36

(note that the rounding means that some haplotypes with trace non-African proportions are now ~0)

So what did I find? I carry the most common non-African haplotype, B001. But here’s the interesting thing: I found that my sibling carries one copy of the B006 haplotype! So at least one of my parents has at least one copy of that haplotype. I find this particularly of interest because of dystrophin’s phenotypic consequences in terms of muscle development. I have one sibling whose results are going to come in soon who happens to resemble me a great deal physically…except for the fact that while I am gracile, they are robust. You can guess my amusement if it turns out that this sibling carries the Neandertal haplotype on this locus!

Note: Credit to Ted Kandell for the “leg work” in the 23andMe forums.

(Republished from Discover/GNXP by permission of author or representative)
 
No Items Found
Razib Khan
About Razib Khan

"I have degrees in biology and biochemistry, a passion for genetics, history, and philosophy, and shrimp is my favorite food. If you want to know more, see the links at http://www.razib.com"