My father is officially more closely related to a 50 thousand year old Neanderthal than to several 1.3 thousand year old modern humans!

As a long-time advocate of Neanderthals being the same species as humans, I was very happy a couple of years ago to find out through a 23andme analysis of my DNA that I’m 3.3% Neanderthal. That put me in the 99th percentile for East Asians, and probably 99th percentile overall. Since the 23andme methodology presumes that sub-Saharan African populations have no Neanderthal admixture (using those populations as the baseline for estimating percentage), the estimated contribution is conservative, because gene flow also moved into Africa, not only out of it. The actual Neanderthal contribution to my genome is undoubtedly higher than 3.3%. I’m certain that with future sequencing of even more DNA from Neanderthals and other archaic homo sapiens, we will find more surprises.
My biggest surprise came today when I was playing around with my dad’s genome on GEDMatch. I was comparing various people’s genomes to the Altai Neanderthal (Siberia, 50,000 years ago) and Hinxton 2 (Britain, 1,300 years ago). My dad, who according to 23andme also has an extremely high Neanderthal contribution (3.1%), actually shares many more SNPs (1cM, 100SNPs parameters) with the Altai Neanderthal than I do. I have 4.3cM in total (only counting segments larger than 1cM) with 756 SNPs, and my dad has 9.4cM and 1034 SNPs. I quickly compared my dad’s numbers to a few other modern samples, and my dad has still significantly more Altai Neanderthal DNA. The real shocker came when I compared my dad’s genome to Hinxton 2. There are no shared segments above the 1.0cM threshold! This is really amazing given that the Hinxton 2 skeleton is an anatomically modern human being from medieval Britain, while the Altai Neanderthal is much more distant in time and a different sub-species. I, in contrast, do share many more segments with the Hinxton 2 individual at the 1.0cM threshold than I do with the Altai Neanderthal. I then cross-checked my father with other ancient DNA samples. Amazingly, he doesn’t share any segments above the 1cM threshold with several other anatomically modern humans (Hinxton 3, Hinxton 5, Gokhem 2) even though he shares segments with the Altai Neanderthal. I, in contrast, share at least one segment with all other anatomically modern homo sapiens in the ancient DNA database at the 1.0cM threshold.
Of course, my dad is much more related to most other anatomically modern homo sapiens in the ancient DNA database, so he is definitely much more human than Neanderthal.  Still, it underscores the fact that we should not categorically define ourselves as always being more genetically similar to every single anatomically modern homo sapiens than to an individual from an “archaic” sub-species.

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