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Wednesday, July 16, 2014

Model yourself as a mixture of ancient genomes


This is really easy and should work well for most personal genomics customers (ie. those of European ancestry and with data files from 23andMe, FTDNA and AncestryDNA).

First of all, make sure you have your Eurogenes K15 ancestry proportions from GEDmatch. Then do the following:

- download the 4 Ancestors Oracle (here)

- download the Eurogenes ancient genomes datasheet (here)

- place everything into the same directory

- double click of the 4 Ancestors Oracle icon (the big red number 4)

- select the Eurogenes K15 ancient genomes datasheet

- type your Eurogenes K15 ancestry proportions into the fields provided

- hit the go button and let it rip

I'm not sure I'm allowed to upload the 4 Ancestors Oracle online, but I couldn't find the original link, so let's assume for the time being that I am. In any case, many thanks to Alexandr Burnashev for this great tool.

You'll also find some modern populations in the datasheet, and I chose those for very good reasons. Most of those reasons are covered in this Eurogenes blog post: Ancient human genomes suggest (more than) three ancestral populations for present-day Europeans.

Obviously, you can edit the datasheet to explore more options by removing or adding individuals and populations. A spreadsheet of Eurogenes K15 population averages is available here. The oracle settings can also be tweaked in a couple of ways to fine tune the results.

If the calculator crashes, try replacing the periods with commas in both the datasheet and your ancestry proportions.

Please keep checking this post, because I'll attempt to update the datasheet at the link above every time a new ancient genome is published and has enough markers available to be tested with the Eurogenes K15. Eventually we might end up with a tool that covers most of the continents and many periods of history and prehistory.

I've done similar analyses of a variety of ancient genomes. For instance, StoraFörvar11, or SfF11, from Mesolithic Sweden came out 3/4 La Brana-1 and 1/4 MA-1, which translates to 3/4 Western European Hunter-Gatherer (WHG) and 1/4 Ancient North Eurasian (ANE), and lines up well with results reported recently for Swedish hunter-gatherers in scientific literature. You can see the full analysis StoraFörvar11 and a few other ancient genomes at the links below.

Analysis of Mesolithic Swedish forager StoraFörvar11

More ancient genomes from Sweden: Pitted Ware forager Ajvide58 and TRB farm girl Gokhem2

4 Ancestors Oracle results for Anzick-1, La Brana-1 and MA-1

I'm still trying to anwser a whole lot of e-mails so I won't be monitoring this post for a while. But please feel free to share your results and any tips you might have in the comments below.

Wednesday, March 19, 2014

Updated Eurogenes K13 and K15 population averages


I just sent off a new population averages spreadsheet for the popular Eurogenes K13 test to GEDmatch. When added to the analysis, the updated data should result in more fine grained and accurate ancestry predictions for many people, especially Northwest, East and South Europeans. Here's the spreadsheet:

Eurogenes K13 population averages

The Fst (genetic) distances between the K13 ancestral populations can be seen here. Below are a couple of cluster trees of West Eurasian populations based on the data. Note also the presence of two ancient genomes, La Brana-1 and MA-1, among the modern samples. I'm actually very impressed how accurate their placings are on the trees.

MA-1, the 24,000 year-old Siberian, is sitting between Eastern Europe and the North Caucasus, which is exactly where he was on a PCA in Lazaridis et al. (see here). On the other hand, La Brana-1, the 7,000 year-old Iberian, is showing strong affinity to circum-Baltic groups, like southwest Finns and northern Swedes, which correlates well with the results from Olalde et al. (see here and here).





Update 22/03/2014: Here's an MDS of Eurasia and the Americas, courtesy of one of my project members. It's actually based on population averages from the Eurogenes K15 test, which I've also just updated (see spreadsheet here). I haven't yet sent these off to GEDmatch, but will when the Ad-mix tools are back online. Note that this MDS also features the other two ancient genomes published recently, Anzick-1 and Saqqaq.


Citations...

Raghavan et al., Upper Palaeolithic Siberian genome reveals dual ancestry of Native Americans, Nature, (2013), Published online 20 November 2013, doi:10.1038/nature12736

Olalde et al., Derived immune and ancestral pigmentation alleles in a 7,000-year-old Mesolithic European, Nature (2014), doi:10.1038/nature12960

See also...

4 Ancestors Oracle results for Anzick-1, La Brana-1 and MA-1

PCA of five ancient genomes


Saturday, December 28, 2013

EEF-WHG-ANE test for Europeans


This is a test that attempts to fit you to the three inferred prehistoric European populations as described in this recent preprint. The relevant Excel file can be downloaded here, and all you have to do is stick your Eurogenes K13 results into the fields provided to get the EEF-WHG-ANE ancestry proportions. A modified version for Near Eastern and Southeast European users can be accessed here.

The test is based on correlations between the average levels of the Eurogenes K13 and the ancient components among selected European populations (see here). Below is a brief description of each of the ancient components.

Early European Farmer (EEF): apparently this is a hybrid component, the result of mixture between "Basal Eurasians" and a WHG-like population possibly from the Balkans. It's based on a 7500 year old Linearbandkeramik (LBK) sample from Stuttgart, Germany, but today peaks at just over 80% among Sardinians.

West European Hunter-Gatherer (WHG): this ancestral component is based on an 8,000 year old forager from the Loschbour rock shelter in Luxembourg, who belonged to Y-chromosome haplogroup I2a1b. However, today the WHG component peaks among Estonians and Lithuanians, in the East Baltic region, at almost 50%.

Ancient North Eurasian (ANE): this is the twist in the tale, a component based on a 24,000 year old Upper Paleolithic forager from South Central Siberia, belonging to Y-DNA R*, and known as Mal'ta boy or MA-1. This component was very likely present in Southern Scandinavia since at least the Mesolithic, but only seems to have reached Western Europe after the Neolithic. At some point it also spread into the Americas. In Europe today it peaks among Estonians at just over 18%, and, intriguingly, reaches a similar level among Scots. However, numbers weren't given in the paper for Finns, Russians and Mordovians, who, according to one of the maps, also carry very high ANE, but their results are confounded by more recent Siberian (ENA) admixture.

It's important to note that this test is only likely to be accurate for people of European ancestry, and indeed only those who aren't outliers from the main European clines of genetic diversity. For details of what that means, please consult the aforementioned paper. However, roughly speaking, if you're of European origin and don't score more than 3% East Asian, Siberian, Amerindian, South Asian, Oceanian, Northeast African and/or Sub-Saharan admixture, then you should get a coherent result. Users from the Near East and Caucasus should run the version specifically designed for them, while those from Southeastern Europe might find it useful to run both calculators and then compare the results.

Thanks to project member DESUK1 for putting this together at such short notice, and MfA for the modified version. Please post your results in the comments section below and state your ancestry when you do. This will help us to improve the accuracy of the test. My results make perfect sense, considering my Polish ancestry, relative to those of the reference samples (see here and here).

EEF 42.012706
WHG 40.52702615
ANE 17.46026785

Below that is a PCA courtesy of project member PL16, based on the EEF-WHG-ANE test results for selected populations. The positions of the ancestral EEF, WHG and ANE groups reflect the PCA loadings (see here).



This is my interpretation of who these components represent. Of course, this model might change when more ancient genomes are analyzed.

WHG and WHG/ANE: indigenous European hunter-gatherers
EEF: mixed European/Near Eastern Neolithic farmers
ANE/WHG: Proto-Indo-European invaders from the Eastern European steppe
ENA/ANE: early Uralics from the Volga-Ural region
EEF/WHG/ANE: late Indo-Europeans (ie. Celts, Germanics and Slavs)

Citation...

Iosif Lazaridis, Nick Patterson, Alissa Mittnik, et al., Ancient human genomes suggest three ancestral populations for present-day Europeans, bioRxiv, Posted December 23, 2013, doi: 10.1101/001552

See also...

Ancient human genomes suggest (more than) three ancestral populations for present-day Europeans

Ancient North Eurasian (ANE) levels across Asia

Thursday, November 21, 2013

Updated Eurogenes K13 at GEDmatch


The old Eurogenes K13 has been replaced by a new model with different, and hopefully more robust, ancestral clusters. The new version also includes Oracles as well as 2D and 3D Principal Component Analyses (PCA). The K13 population averages and genetic (Fst) distances between the inferred ancestral clusters are available here and here, respectively.

GEDmatch > Ad-Mix Utilities > Eurogenes > K13

Below is a 2D PCA based on the average K13 results of the European and Asian reference populations, courtesy of project member PL16.


Thus, Eurogenes now has four tests at GEDmatch with Oracles: the Jtest, EUtest, EUtest V2 and the K13. It's useful to keep in mind that these tests will differ in their interpretation of the data, and perhaps accuracy, depending on the ancestry of the user. For instance, the new K13 should be more useful for Central and South Asians than any of the others, because it features new reference samples from these regions.

Monday, October 7, 2013

Eurogenes K15 now at GEDmatch


This new test is essentially an upgraded version of the EUtest. Unlike the original, it includes an Amerindian component and five native reference populations from North and Central America. So obviously it should be a lot more useful for users from the New World who are wondering about Amerindian admixture.

GEDmatch > Ad-Mix Utilities > Eurogenes > Eurogenes EUtestV2 K15

I just tried it myself, and have say that the 4-Ancestors Oracle results were impressive. In other words, they were very accurate based on what I know about my recent ancestry. On the other hand, I'd say the default Oracle was picking up more ancient gene flows. However, this might not be the case for everyone, so let's hear some feedback, discuss the outcomes, and perhaps tweak the settings if necessary.

One of the most important things to keep in mind is to ignore all results under 1%. These are likely to be noise.

Here are the populations averages and Fst distances between the ancestral components. Below are spatial maps of the main West Eurasian components courtesy of Gui (FR7): Baltic, North Sea, Atlantic, East Euro, West Med, East Med, West Asian.










Saturday, March 9, 2013

Eurogenes K36 at GEDmatch


I've just put together a new test for GEDmatch called the Eurogenes K36. Obviously, the K36 means that it features thirty six ancestral clusters. It probably won't include any Oracles, mostly because the Calculator Effect would render these useless if they were based on the average results of the reference samples (see the sheet here for details), and it'd be very time consuming for me to test a wide variety of other samples in supervised mode using thirty six sets of allele frequencies.

The main purpose of the Eurogenes K36 is to help users unravel the ethnic origins of local areas of their genomes (aka. half-segments), hence the high number of ancestral categories, some of which are very specific. In other words, the test is mainly a chromosome painting utility. It's accessible via the GEDmatch Ad-Mix link below:


GEDmatch > Ad-Mix page > Eurogenes > Eurogenes K36


An important point to keep in mind is not to take the ancestry proportions too literary. If you're, say, English, and you get an Iberian score of 12% this doesn't actually mean you have recent ancestry from Spain or Portugal. What it means is that 12% of your alleles look typical of the reference samples classified as Iberian, and this figure might only indicate recent Iberian admixture if it's clearly higher than those of other English users.

Another way to look at it is that the ancestry proportions are like map coordinates, and they'll place you with a very high degree of accuracy on a genetic map featuring other users. Indeed, please feel free to post your scores and ancestry details in the comments below to help others get an idea of what their results might represent. My results are listed below. The scores put me squarely in Poland relative to those of other European samples I've run, which is correct.


Also worth mentioning is that this test focuses on much deeper ancestry than the Ancestry Composition at 23andMe. Hence, I expect that many Europeans will score a few percent in non-European clusters. However, like many ADMIXTURE results, this could give us strong hints about population movements into Europe during prehistory and early history, so it's worth keeping an eye on.


Monday, December 3, 2012

4-Ancestors Oracle at GEDmatch


The Jtest and EUtest at GEDmatch now include a new tool called the 4-Ancestors Oracle (aka. Oracle-4), as well as the 3D PCAs I promised earlier. Oracle-4 will attempt to pinpoint your ethnic group of origin, and then also work out the most likely combinations of two, three and four ancestral populations which make up your genome. However, this doesn't mean the results will actually show your ethnic group, or those of your parents (in dual mode) or grandparents (4-way mode). They might for many people, but for others they'll reflect the best possible outcomes from the reference samples available.

GEDmatch Ad-Mix Utilities

Enjoy, and feel free to give feedback to John at GEDmatch if you think it might be useful (but please don't spam his account).