Search This Blog

Thursday, September 6, 2018

Global25 nMonte runner


Those of you who are having trouble with making use of your Global25 coordinates on your own computers, please be aware that there's an online tool that might be of help. It's called the Global25 nMonte runner and very easy to use. For more info see here.


See also...

Genetic ancestry online store (to be updated regularly)

Modeling genetic ancestry with Davidski: step by step

If you're using my tools to find Jewish ancestry please read this

Saturday, August 25, 2018

Global25 workshop 3: genes vs geography in Northern Europe


To produce the intra-North European Principal Components Analysis (PCA) plot below, download this datasheet, plug it into the PAST program, which is freely available here, then select all of the columns by clicking on the empty tab above the labels, and choose Multivariate > Ordination > Principal Components or Discriminant Analysis.


I'd say that the result more or less resembles a geographic map of Northern Europe. Of course, if you're in the possession of your own personal Global25 coordinates, you can add yourself to this plot to check whether your position matches your geographic origin.

Please keep in mind, however, that the vast majority (>90%) of your ancestry must be from north of the Alps, Balkans and Pyrenees to obtain a sensible outcome. Also please ensure that all of the columns in the datasheet are filled out correctly, including the group column, otherwise your position on the plot will be skewed.

See also...

Global25 workshop 1: that classic West Eurasian plot

Global25 workshop 2: intra-European variation

Global25 workshop 3: genes vs geography in Northern Europe

Global25 PAST-compatible datasheets

Modeling genetic ancestry with Davidski: step by step

Genetic ancestry online store (to be updated regularly)

Sunday, August 12, 2018

Global25 workshop 2: intra-European variation


Even though the Global25 focuses on world-wide human genetic diversity, it can also reveal a lot of information about genetic substructures within continental regions.

Several of the dimensions, for instance, reflect Balto-Slavic-specific genetic drift. I ensured that this would be the case by running a lot of Slavic groups in the analysis. A useful by-product of this strategy is that the Global25 is very good at exposing relatively recent intra-European genetic variation.

To see this for yourself, download the datasheet below and plug it into the PAST program, which is freely available here. Then select all of the columns by clicking on the empty tab above the labels, and choose Multivariate > Ordination > Principal Components.

G25_Europe_scaled.dat

You should end up with the plot below. Note that to see the group labels and outlines, you need to tick the appropriate boxes in the panel to the right of the image. To improve the experience, it might also be useful to color-code different parts of Europe, and you can do that by choosing Edit > Row colors/symbols. Of course, if you have Global25 coordinates you can add yourself to the datasheet to see where you plot.


Components 1 and 2 pack the most information and, more or less, recapitulate the geographic structure of Europe. However, many details can only be seen by plotting the less significant components. For instance, a plot of components 1 and 3 almost perfectly separates Northeastern Europe into two distinct clusters made up of the speakers of Indo-European and Finno-Ugric languages.


This plot might also be useful for exploring potential Jewish ancestry, because Ashkenazi, Italian and Sephardi Jews appear to be relatively distinct in this space. Thus, people with significant European Jewish ancestry will "pull" towards the lower left corner of the plot. For example, someone who is half Ashkenazi and half German will probably land in the empty space between the Northwest Europeans and Jews.

See also...

Global25 workshop 1: that classic West Eurasian plot

Global25 workshop 3: genes vs geography in Northern Europe

Global25 PAST-compatible datasheets

Modeling genetic ancestry with Davidski: step by step

Genetic ancestry online store (to be updated regularly)

Global25 workshop 1: that classic West Eurasian plot


In this Global25 workshop I'm going to show how to reproduce, more or less, that classic plot of West Eurasian genetic diversity seen regularly in ancient DNA papers and at this blog (for instance, here). To do this you'll need the datasheet below, which I'll be updating regularly, and the PAST program, which is freely available here.

G25_West_Eurasia_scaled.dat

This is what you'll get if you follow my instructions to the letter. Note the fairly strong correlation with geography. I think this is impressive for so many reasons.

OK, so, download the said datasheet, plug it into PAST, select columns 1 to 8, and go to Multivariate > Ordination > Principal Components. Here's a screen cap of me doing it:


The initial output won't resemble my plot above. So you'll need to place PC2 on the X axis, PC1 on the Y axis, and set the image size to 1206x706. After doing that, you should end up with exactly this:


Then, export the image, flip it horizontally with whatever imaging software that can do the job, and that's it, unless you want to add some labels like I did. Feel free to ask questions and make suggestions in the comments below.

See also...

Global25 workshop 2: intra-European variation

Global25 workshop 3: genes vs geography in Northern Europe

Global25 PAST-compatible datasheets

Modeling genetic ancestry with Davidski: step by step

Genetic ancestry online store (to be updated regularly)

Global25 PAST-compatible datasheets


I'm planning to run regular workshops over the next few months on how to get the most out of Global25 data with various programs, and expecially PAST (see here). So if you have Global25 coordinates, please stay tuned.

To that end, I've put together four color-coded, PAST-compatible Global25 datasheets with thousands of present-day and ancient samples, available at the links below:

Global_25_PCA.dat

Global_25_PCA_pop_averages.dat

Global_25_PCA_scaled.dat

Global_25_PCA_pop_averages_scaled.dat

PAST is an awesome little statistical program and simple to use. The manual is available here. To kick things off, here's a quick guide how to run a Neighbor Joining tree on your Global25 coordinates:

- download the Global_25_PCA_pop_averages_scaled.dat from the last link above

- open the dat file with something a little more advanced than Windows notepad, like, say, TextPad (see here)

- stick your scaled coordinates at the bottom of the sheet, so that they look exactly like those of the other samples, except give yourself an original symbol, like, say, a black star

- open the edited dat file with PAST and choose all of the columns and rows by clicking the empty tab above the labels

- then, at the top, go to Multivariate > Clustering > Neighbor joining

After a few seconds you should see a nice, color-coded tree like the one below, except you'll also be on it, in black text. I'm very happy with these results, by the way. As far as I can see, all of the populations and individuals cluster exactly where they should.


Those of you who are already very proficient in using PAST, feel free to go nuts with these new datasheets and show us the results in the comments below. I'll try to put together a workshop for beginners within the next couple of weeks.

See also...

Global25 workshop 1: that classic West Eurasian plot

Global25 workshop 2: intra-European variation

Global25 workshop 3: genes vs geography in Northern Europe

Modeling genetic ancestry with Davidski: step by step

Genetic ancestry online store (to be updated regularly)

Monday, March 19, 2018

If you're using my tools to find Jewish ancestry please read this


It's come to my attention that many people are still using the Jtest and taking the results very seriously. Indeed, perhaps too seriously.

Also, some users are doing weird stuff with the Jtest output in an attempt to estimate their supposedly "true" Ashkenazi ancestry proportions, like multiplying their Ashkenazi coefficient by three, because Ashkenazi Jews "only" score around 30% Ashkenazi in this test. Ouch! Please don't do that!

Let me reiterate that this test was only supposed to be a fun experiment. It was never meant to be the definitive online Ashkenazi ancestry test. And even as fun experiments with ADMIXTURE go, it's now horribly outdated, and probably useless for anyone with less than 15-20% Ashkenazi ancestry.

So it might be time to move on. If you really want to confirm your Jewish ancestry, either or both Ashkenazi and Sephardi, then you need to look at much more powerful and sophisticated options. One of these options is the Global25 analysis (see HERE), which can pick up minor Jewish ancestry of just a few per cent. But it's not free (USD $12), and it's a DIY test that requires a bit of time and effort to get the most out of it. Also, you'd need to send me your autosomal file so that I can estimate your Global25 coordinates. But I can help you get started and even quickly check if you have any hope at all of confirming Jewish ancestry.

If, for whatever reason, you'd rather not take advantage of the Global25 offer, because, say, you don't want to share your data with me, then it might be an idea to join the Anthrogenica discussion board and ask the experienced members there about other options [LINK].

In any case, whatever you choose to do, please remember the following points, and feel free to share them with others who are still using the Jtest:

- do not multiply your Jtest Ashkenazi score by 3 in an attempt to find your "true" Ashkenazi ancestry proportion, because this won't work for the vast majority of users

- but do compare your Jtest Ashkenazi score to those of other people of the same or very similar ancestry to yours to get a rough idea whether you might have any Ashkenazi ancestry (the Jtest population averages will be useful for this, see here)

- if you're still not sure what your Jtest results mean, then just focus on your Jtest Oracle-4 output at GEDmatch, and if you don't see AJ at the top of the oracle list, then this is a strong signal that you don't have substantial Ashkenazi ancestry

See also...

Global25 workshop 1: that classic West Eurasian plot

Global25 workshop 2: intra-European variation

Global25 workshop 3: genes vs geography in Northern Europe

Global25 PAST-compatible datasheets

Modeling genetic ancestry with Davidski: step by step

Genetic ancestry online store (to be updated regularly)

Sunday, February 18, 2018

The powerful Global 25 now available via the Eurogenes genetic ancestry online store


Following a rigorous testing phase, the awesome Global 25 analysis is now available via my genetic ancestry online store for $12 USD (see here). What's so awesome about this test, you might ask? See here and here.


Please send your request, autosomal genotype data (from AncestryDNA, FTDNA, LivingDNA, MyHeritage or 23andMe) and money (via PayPal) to eurogenesblog at gmail dot com.

However, note that this test is free for anyone who already has Global 10 coordinates (see here). That's right, if you already have Global 10 coordinates, all you have to do is to send me your data and say what it's for. Simple as that.

See also...

Global25 workshop 1: that classic West Eurasian plot

Global25 workshop 2: intra-European variation

Global25 workshop 3: genes vs geography in Northern Europe

Global25 PAST-compatible datasheets

Modeling genetic ancestry with Davidski: step by step