The 23andMe blog, the Spittoon, has a description of their new technique to use 23andMe SNPs to estimate any customer's fraction of Neandertal: "Find your inner Neanderthal".
The result is a rough-and-ready numerical estimate of your Neandertal ancestry fraction. For me it's 2.5 percent. Gretchen is 3 percent, and she's been lording it over me all day.
The estimate is the work of Eric Durand, who broke ground on the D-statistic method for finding introgression from archaic genomes
So far, all estimates of Neandertal (or other archaic human) ancestry have come from the proportion of a genome (or genotypes from a genome) that are shared and derived with Neandertals. That includes the results I've been posting here for the 1000 Genomes Project samples this week.
The next step is to uncover exactly which parts of a person's genome have come from Neandertal ancestors. To discover this, we have to further determine which shared alleles come from recent introgression as opposed to ancient incomplete lineage sorting. We have been working very hard on that problem here, as you'll see, and it has been an important aspect of our work in pigmentation genes in the archaic genomes.
If you have been considering getting your genotypes from 23andMe, it has become a very good time to do this. The overall fraction of your DNA derived from Neandertals is only the beginning. Soon we'll be able to specify which parts, and in a few cases we'll have a good guess as to what difference it makes. If you want to participate in this research, I'm hoping to gather as many interested people as I can -- so keep your eyes here over the next month.
And if you are interested in having your genotypes done, feel free to use my link to the 23andMe promotion. I've been very happy with their way of presenting the genotypes and their updates, and know many other people who have also found it interesting. As I wrote a couple of years ago, it's not something to spend your food money on, but it does have an entertainment value. And the potential to be an active research participant.