Neandertal (haplotype) in the family!

By Razib Khan | January 27, 2011 11:41 am

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) :


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

(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.

CATEGORIZED UNDER: Genetics, Genomics, Personal Genomics

Comments (11)

  1. sv

    Interesting post. Like you, I have the rather common B001.

  2. In The Spittoon (23andme blog) there was a post on Neanderthal admixture with some interesting comments reporting on the SNPs associated to alleles of putative Nearderthal ancestry.
    Also, if you upgrade to v3, you’ll end up having 30,000 more SNPs covered than people just doing the v3:

    V2 only: 576,000 SNPs
    V3 only: 967,000 SNPs
    V2 + V3 (upgraded): 996,000 SNPs

    I think John Hawks would enjoy the pride with which people report their putative Neanderthal ancestry! I can’t wait to get my 23andme results.

  3. I’m B019. I just got my 23andme results and I’m trying to make sense of all of this…

  4. Dragon Horse

    I’m African American and I’m B1

    My fiancee is Swiss is homozygous on ever SNp and is also B1. LOL

    My ex-wife (Japanese) could be B06 or B004, she his heterozygous for all but three, and none of her family has been tested.

    Not sure it is exciting to know I’m part nonHomo Sapien Sapien (aka Cave Man) or not. :-O

  5. Que-z

    This two are the same. What gives?

    B006 AATGAATTT – Archaic or Neanderthal
    B012 AATGAATTT African ancient branch

  6. This two are the same. What gives?

    can’t distinguish with the SNPs 23andme has. so you have to go with geography here.

  7. Mary

    I’m B001 for both copies of gene. My husband is the rarer B003, but then he plots with the French on the ancestry painting. Ha!

    Thanks, Razib, for this bit of fun.

  8. Zohar

    I’m B0001. That makes me modern?


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About Razib Khan

I have degrees in biology and biochemistry, a passion for genetics, history, and philosophy, and shrimp is my favorite food. In relation to nationality I'm a American Northwesterner, in politics I'm a reactionary, and as for religion I have none (I'm an atheist). If you want to know more, see the links at


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