Monday, May 8, 2017
An nMonte and 4mix guide for the participants of the Basal-rich K7 and/or Global 10 tests of the Eurogenes Project
Copied from a thread at the Anthrogenica forum because unfortunately it seems that a lot of people can't access the post: This is an nMonte and 4mix guide I have written for people who donated to the Eurogenes Project in order to take part in the Basal-rich K7 and/or Global 10 tests of that project and subsequently received their test results. For information on how to participate in one or both of the Basal-rich K7 and Global 10 tests, see the link below: Fund-raising offer: Basal-rich K7 and/or Global 10 genetic map In your results you receive from Davidski by email, you are provided with your Basal-rich K7 component percentages and your position on the Basal-rich K7 PCA if you took the Basal-rich K7 test, and your Global 10 PCA coordinates and your position on the Global 10 PCA if you took the Global 10 test. You will need your Basal-rich K7 component percentages and/or Global 10 PCA coordinates in order to make use of nMonte and 4mix, which allow you to be modeled as a mix different populations in varying ancestry percentages and varying distance levels based on either of your Basal-rich K7 and Global 10 results. You can download nMonte and 4mix from these links respectively: nMonte 4Mix Because that it can run multiple targets at the same time, I gave the link to 4mix_multi rather than classical 4mix. They are basically the same in all other aspects. In order to use nMonte and 4mix you need to have the R software installed on your PC. You can download it from one of the mirrors here: CRAN mirrors Making a target file for Basal-rich K7: Open Notepad and copy and paste the Basal-rich K7 component names and your Basal-rich K7 component percentages along with your name in this format: Basal-rich K7 spreadsheet Global 10 datasheet Save the input file as input. Here is an example of a Basal-rich K7 input file for nMonte: https://www.familytreedna.com/groups/anatol-balkan-caucas/about https://www.facebook.com/groups/800912433320422/
Sunday, March 19, 2017
I'm now taking donations for 2017. Anyone who donates $12 USD or $16 AUD, or more, will get the Basal-rich K7 ancestry proportions. Of course, you'll need to send me your genotype data for that to happen (Ancestry.com, FTDNA or 23andMe).
D(Yoruba,Iran_Neolithic)(Villabruna,AfontovaGora3) 0.0223 Z 2.812On the other hand, the Basal-rich K7 models the early Zagros farmers as 39.05% Ancient North Eurasian and 56.67% Basal-rich (which is probably a composite of Basal Eurasian and something Villabruna-related). To me this appears to be the more sensible solution. Moreover, Lazaridis et al. 2016 characterized South Caspian forager Iran_HotuIIIb as more Basal Eurasian than the early Zagros farmers (Supplementary Information 4). The Basal-rich K7, on the other hand, shows the opposite. The D-stat below suggests that the Basal-rich K7 is closer to the truth.
D(Chimp,Ust_Ishim)(Iran_Neolithic,Iran_Hotu) 0.0156 Z 1.337There are other such examples, and I might post them in the comments. In any case, the point I'm making is that the Basal-rich K7 is a solid piece of work and it's likely to remain relevant for a long time. Indeed, I'll be updating the Basal-rich K7 spreadsheet regularly as new ancient samples roll in, which means that you'll be able to model yourself as newly sampled ancient populations using the Basal-rich K7 ancestry proportions (for instance, see here). The only problem with this test is that it's optimized for Eurasians. As a result, it might be sensible for anyone with significant (>5%) Sub-Saharan ancestry to skip the Basal-rich K7 and just ask for the Global 10 genetic map and coordinates. Global 10 coordinates to model your ancient and recent fine-scale ancestry, just as you would using mixture proportions. In fact, I'd say the Global 10 coordinates are more useful in this respect than any mixture test, including the Basal-rich K7. Thanks in advance for your support. Keep in mind that the more cash I raise the busier things will be on this blog in 2017, which, by all accounts, is shaping up to be the year for ancient DNA.