The first thing you need to know about the
Global25 is that I update the relevant datasheets regularly, usually every few weeks, but they're always at these links:
Global25 datasheet ancient scaled
Global25 pop averages ancient scaled
Global25 datasheet ancient
Global25 pop averages ancient
...
Global25 datasheet modern scaled
Global25 pop averages modern scaled
Global25 datasheet modern
Global25 pop averages modern
Global25 data for samples from a variety of papers that have been published recently will eventually be incorporated into the main datasheets linked above, but the process might take several weeks or even months. In the meantime, feel free to use the temporary datasheets below. Thanks for your patience.
Allentoft 2023
Chylenski 2023
Jeong 2024
Koptekin 2022
Olalde 2023
Peltola 2022
Penske 2023
Posth 2023
Sirak 2024
Skourtanioti 2023
Stolarek 2023
Varela 2023
Wang 2023
Yu 2023
Each sample has a population code and an individual code. The population codes represent the countries, ethnic groups and/or archeological affinities of the samples, and I often modify these codes to suit my needs. On the other hand, the individual codes are unique to most of the samples and I usually don't change them.
So if you'd like to know more details about the samples try searching for their individual codes via a decent online search engine. Basic information about many of the samples is also available in the "anno" files
here.
The main purpose of the Global25 is to provide data for mixture modeling. In other words, for estimating ancestry proportions, both ancient and modern (see
here). This can be done on your computer with the R program and the nMonte R script, or online with a couple of different tools, which I discuss below.
If you don't have R installed on your computer, you can get it
here, while nMonte is available
here. For this tutorial please download nMonte and nMonte3, and store them in your main working folder (usually My Documents).
Once you have R set up, make sure its working directory is the same place where you stored nMonte. You can check this in R by clicking on "File" and then "Change dir". Additionally, you'll need two nMonte input files in the working directory titled "data" and "target". Examples of these files are available
here. We'll be using them to test the ancient ancestry proportions of a sample set from present-day England.
Before you can begin the analysis you need to first call the nMonte script by typing or copy pasting
source('nMonte.R') into the R console window, and then hitting "enter" on your keyboard. This is what you should see in the R console window afterwards.
To start the mixture modeling process, type or copy paste
getMonte('data.txt', 'target.txt') into the R console window, hit "enter", and wait for the results. After a short time, probably less than a minute or two, you should see this output.
The data and target files contain population averages. And, as you can see, the results that these population averages have produced are in line with what one would expect from such a model focusing on the genetic shifts in Northern Europe during the Late Neolithic. Very similar ancient ancestry proportions have been reported for the English and other Northern Europeans recently in scientific literature.
However, when focusing on exceptionally fine-scale genetic variation that isn't reflected too well in the Global25 population averages, a more effective strategy
might be to use multiple individuals from each reference population and let nMonte3 aggregate and average the inferred ancestry proportions.
This is often the case when attempting to model ancestry proportions for more recent periods, such as the Middle Ages. So let's try this with the English sample set using a modified data file, which is available
here.
Replace the old data file with the new one in your working directory, and, like before, copy paste into the R console window the following two commands, hitting "enter" after each one:
source('nMonte3.R') and
getMonte('data.txt', 'target.txt'). This is what you should eventually see.
It's difficult to say how accurate these estimates are. But they look more or less correct considering the limited and less than ideal reference samples. For instance, the individuals labeled SWE_Viking_Age_Sigtuna are supposed to be stand ins for Danish and Norwegian Vikings, but they're a relatively heterogeneous group from Sweden, possibly with some British or Irish ancestry, so they might be skewing the results.
However, I'll be adding many more ancient samples to the Global25 datasheets as they become available, including lots of new Vikings, which should greatly improve the accuracy of these sorts of fine-scale mixture models.
An exceedingly simple, yet feature-packed, online tool ideal for modeling ancestry with Global25 coordinates is the VahaduoJS. It's freely available
HERE, and it also works offline after downloading the web page. Just copy paste the coordinates of your choice under the "source" and "target" tabs, and then mess around with the buttons to see what happens. The screen caps below show me doing just that.
However, it's important to note that the Global25 is a Principal Component Analysis (PCA), so it makes good sense to also use it for producing PCA graphs. To do this just plot any combination of two or three of its Principal Components (PCs) to create 2D or 3D graphs, respectively. This can be done with a wide variety of programs, including PAST, which is freely available
here.
To produce a 2D graph, open a Global25 datasheet in PAST, choose comma as the separator, highlight any two columns of data, click on the "Plot" tab and, from the drop down list, pick "XY graph". Below is a series of graphs that I created in exactly this way. I also color coded the samples according to their geographic origins. This was done by ticking the "Row attributes" tab.
PAST can also be used to run PCA on subsets of the Global25 scaled data to produce remarkably accurate plots of fine-scale population structure. For instance, here's a plot based on present-day populations from north of the Alps, Balkans and Pyrenees.
To try this create a new text file with your choice of populations from the Global25 scaled datasheet, open it with PAST and choose Multivariate > Ordination > Principal Components Analysis. I've already put together several datasheets limited to European, Northern European, West Eurasian and South Asian populations. They're available at the links below along with more details on how to run them with PAST.
Global25 workshop 1: that classic West Eurasian plot
Global25 workshop 2: intra-European variation
Global25 workshop 3: genes vs geography in Northern Europe
The South Asian cline that no longer exists
Another free, easy to use online tool that works with Global25 coordinates is the Vahaduo Global25 Views [
LINK]. Below is a screen cap of me checking out one of the many PCA that it offers.
And if you're fond of tree-like structures as a means to describe fine-scale genetic variation, please see this blog post...
Global25 workshop 4: a neighbour joining tree
See also...
New Global25 interpretation tools
