My family's Neandertal genes, ii

By Razib Khan | February 1, 2011 5:33 pm

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.

CATEGORIZED UNDER: Genetics, Genomics, Personal Genomics
  • Jeremy

    This is unrelated to your post but I thought you might be interested in this paper published in Social Behavior and Personality

    Are the Shau people in Taiwan of Dutch descent?

    Chin Jung Tu (National United University, Miao-Li, Taiwan, ROC), Bi-Kun Tsai (National Chung-Hsing University, Taichung, Taiwan, ROC), Shu Chun Chang, PhD (National Chung-Hsing University, Taichung, Taiwan, ROC) 2011, 39 (1), 55-64

    In this paper, the culture and origins of the Shau Aborigines of Sun Moon Lake in Central Taiwan are examined. Conclusions presented in this article depend on clues from documents and long-term observation, that reveal that the characteristics of the Shau Aborigines are quite different from those of other aboriginal inhabitants of Taiwan. They lived on islands for a long time, were good at trading, and had a high material living standard, versatile language, and facial features similar to Western people. It is assumed from many reasonable interpretations of questions concerning their cultural characteristics that they may be descended from Dutch preachers and their families in Shaulon, Tainan, who married local Pingpu Aborigines. The Shau fled from Soulang when Zheng Chen-Kung (also known as Coxinja) attacked in 1661, moving to Mattauw, then to Dorcko, Tilaossen, and finally to Lehyee, the territory of Chou Aborigines, where they settled at Laichi for a time. When they discovered Sun Moon Lake, they moved to its island where they are today.

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This blog is about evolution, genetics, genomics and their interstices. Please beware that comments are aggressively moderated. Uncivil or churlish comments will likely get you banned immediately, so make any contribution count!

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 http://www.razib.com

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