Who lives in or near Bradford and can make it to the presentations below? Afterwards can you please report back here about what was said. The sessions are being held next month as part of the 2013 EUROPA conference at the University of Bradford. For details how to book a ticket see the flier here. Thanks in advance.
"The Rise" is an ERC funded project of Early European Bronze Age (2000-3000 BC). While including a range of scientific disciplines, it also represents what is arguably the largest DNA study of ancient human populations to date. The aim is to generate genome-wide data from hundreds of individuals to obtain a high resolution genetic image of the mobility and origin of early Europeans. It is still early days in terms of population genetic analyses, but the many hundred millions of DNA sequences generated so far has provided significant insights into DNA preservation and degradation. This information can assist in defining the genomic potential in "The "Rise" and future projects with similar aims. In the light of these results, I will discuss what is required to take European archaeo-genetics past the traditional mitochondrial haplogroup analyses, and into the era of high-resolution genomics. Is it all just a pipe dream?
Friday 14th June - 15:15–17:00, Dr Morten Allentoft (University of Copenhagen): Profiling the entire genomes of ancient Europeans - a pipe dream or a wonderful challenge?
New evidence from isotopic and ancient DNA has the potential to rewrite large portions of our understanding of the Bronze Age. While much of this work is still in a preliminary stage, there are indications that movement and connections were an important part of being important in this period of time. Not so different from today. Isotopic studies of the Bell Beaker period and several investigations of Bronze Age human remains from central and northern Europe will be discussed and evaluated. Kristiansen’s contribution to this debate in light of some of the new evidence will be considered.
Friday 14th June - 17:00–18:00, Keynote address by Professor Douglas Price (University of Wisconsin): The spread of bronze and the movement of people in prehistoric Europe
The breakthrough of the Nordic Bronze Age (NBA) took place c.1600 BCE in NBA IB, which was also the period when Southern Scandinavia emerged as a cultural koiné in clear outline within Bronze Age Europe. This paper seeks to uncover some of the underlying incentives and historical pathways. Indigenous ore sources were largely ignored, arguably because of a strong cultural tradition for looking south for new materials and inspiration: Desire for bronze and gold objects and the associated metallurgy based on foreign metal were keys to this steady European linkage as well drivers in local change, no doubt, but do not stand isolated. Rich warrior assemblages take centre stage as they hold extraordinary weaponry decorated with, or accompanied by, cosmological symbols. Weapon forms and decoration pinpoint the Carpathian Basin, and secondly the Eurasian steppes, as crucial for the appearance of the NBA as a cultural force in its own right around 1600 BCE. The paper tentatively concludes that in this socio-cultural process of change new warrior ideals were sustained by the transmission of reformed ideas of the constitution of cosmos.
Saturday 15th June - 12:05–12:40, Professor Helle Vandkilde (University of Aarhus): Nordic Bronze Age beginnings
See also...
Hundreds of prehistoric North European skeletons to be genotyped for Y-DNA, mtDNA and autosomal DNA
Full Y-chromosome sequencing is now available to the general public thanks to Rockville-based Full Genomes Corporation. The price is normally $1,499, bit those who jump in early enough will only pay $1,299 (including shipping).
We are currently offering a one of a kind test—not available elsewhere—that will sequence your FULL Y-DNA chromosome. This is the DNA you inherit from your father, and his father and so on, back in time. It will allow you to determine the exact SNP's and STR's you have and how you are related to other family members and members of your community.
The reason I'm shamelessly plugging this company is because it'll be nice to see 23andMe and FTDNA get some real competition so they work a little harder to improve their ancestry services. Moreover, one of the people behind Full Genomes is a regular contact of mine and personal genomics customer from way back, so I have faith that the company will deliver a high quality product. You'll find more info at the link below...
Full Genomes DNA Sequencing
In a new article at my main blog I describe how Europeans became more hunter-gatherer-like genetically after the Neolithic. Yep, after the Neolithic. It's a theory that was entertained by some archaeologists and linguists in the past, but we're now seeing strong signals in ancient and modern DNA data to back it up.
Modern European ADMIXTURE components = Neolithic ecological zones (+ post-Neolithic in-situ expansions)
Update 05/05/2013: I was about to make a GEDmatch ancestry test based on the three Neolithic components described in my post, but then I realized that such a test was already available there, and it's called the Eurogenes K9. All you have to do is re-name several of the components in the following way...
North European > Corded Ware, Single Grave, Battle Axe, Unetice and/or Bohemian Bell Beaker
Mediterranean > Impressed Ware, Cardial Ware, Maritime Bell Beaker and/or Funnelbeaker (TRB)
Caucasus & Southwest Asian > Linearbandkeramik (LBK)
Ancient DNA will tell us one day whether these assumptions are correct. However, please note that the new component names won't be relevant for everyone. For instance, if you're from East Africa or Turkey, then the Caucasus-like admixture you score won't be due to LBK farmers, because they were based in Western and Central Europe.
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.
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).
Following a recent update, the SPatial Ancestry analysis (SPA) software now allows individual users to pinpoint their genetic origins on a Google map (see here). Unfortunately, the allele "model" files used for this purpose only seem to produce accurate results for people of British ancestry.
I suspect the problem with the European model file (europe.model) is that it's based on the POPRES dataset, which includes hundreds of samples from the British Isles and surrounds, but very few or none at all from many other parts of Europe. I'm not sure what the issue is with the world model file, based on the HGDP dataset, but there's definitely an issue, because apparently most people end up in the Atlantic.
As a result, I thought I'd help out and put together a few SPA model files of my own, using my Eurogenes Project dataset, which is now more comprehensive than most academic datasets. But please, in order to get sensible results, only use the files that are at least broadly relevant to your ancestry.
Eurogenes_Eurasian_cline.model - as per the name, this file will plot you along the genetic cline that runs from Europe to the Far East. Most Europeans will land somewhere in Central or Eastern Europe, while most unadmixed East Asians in China or Korea. South Asians will plot somewhere between Europe and South India, depending on the level of the so called Ancestral North Indian (ANI) component in their genomes.
Eurogenes_Finland.model - Finns are difficult to plot correctly on genetic maps when lots of other groups are included, due to their demographic history and eastern admixture. This Finland-specific file attempts to get around such problems. West Finns will land on the Baltic coast, or in the Baltic Sea, while East Finns will plot near Russia, or just over the Russian border.
More model files will appear here in due time. Below are some basic instructions how to run SPA with my model files. There are different ways of doing this, but this is what I do.
Download spa.exe from the SPA website and place it into your WINDOWS folder.
Download the Eurogenes_Eurasian_cline.model zip file, unzip it, and place it into your C: folder.
Download your raw data from 23andMe, unzip it, rename the text file Test.txt, and place it into your C: folder.
Call up the Command Prompt window (cmd). For instance, go to the windows menu in the bottom left of the screen, type cmd into the search field, and double click on cmd.exe.
In your cmd window type the following command: spa --mfile c:\Test.txt --model-input c:\Eurogenes_Eurasian_cline.model --location-output EUC.loc
To split your genome into two, type: spa --mfile c:\Test.txt --model-input c:\Eurogenes_Eurasian_cline.model --location-output EUC.loc -n 2
Go to your user directory to collect the results (C: > Users > Whatever your username is).
Please let me know how it went, so I can make adjustments to the files if needed. However, it's important to understand that placing many people withing the borders of their countries of origin won't be possible, basically due to the fact that modern political borders often don't reflect substructures created by ancient gene flows. This is especially true for groups that don't fall within the normal clines of genetic diversity, like Sardinians and Basques.
Indeed, based on my experiments with this software, I have to conclude that the correlation between genes and geography isn't as tight as has been claimed recently (see here). It's actually very difficult to manipulate the analysis to make sure the vast majority of ethnic groups match their geography.
Therefore, as always, the best way to interpret the results is to compare them with those of other users. For instance, if you're Korean and find yourself just outside of Korea when using the Eurasian cline file, this need not mean you have recent foreign ancestry. In order to test this, check where other Korean samples land, specifically those from the same region as yourself. You're likely to find that they all plot near your pin (or pins in dual mode).
See also...
SPatial Ancestry analysis (SPA) for 23andMe clients (at my other blog)
SPatial Ancestry analysis (SPA) website
The main orientations of human genetic differentiation
Attention: the Jtest and EUtest are now available at GEDmatch. Please see the bottom of the post for more details.
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I recently learned that the new Ancestry Painting at 23andMe will include an Ashkenazi reference group. To be honest, I’m not sure there’s much value in using a genetically bottlenecked population of varied biogeographical origins as a reference in such things. Indeed, the Ashkenazi mainly descend from a few hundred founders, but carry Central European, Eastern European, Middle Eastern, African and probably many other admixtures, as evidenced by their genome-wide and uniparental markers.
That’s quite a problem, because due to their relative inbreeding, they produce strong ancestral clusters in many analyses, like in ADMIXTURE runs. However, these clusters are made up of allele frequencies from a wide range of sources and, paradoxically, it’s the relatively more outbred populations which contributed to the Ashkenazi gene pool at its formative stages that often end up showing Ashkenazi admixture in such tests, despite not having any. I've seen this happen regularly in my experiments with ADMIXTURE and STRUCTURE, and I'm pretty sure I could find an example in a peer reviewed study if I tried.
That’s just how things work with the algorithms we have available to run these sorts of tests. Nevertheless, since 23andMe is incorporating an Ashkenazi cluster into its new painting, I thought I’d try and come up with an Ashkenazi ancestry test to perhaps get a rough idea of what we might expect. I'm using ADMIXTURE in supervised mode, and basically trying to recreate clusters that have shown up in a variety of fine-scale analyses, including my ChromoPainter run of Northern European samples. It’s still a work in progress, but below are links to files that many of you might find useful..
Jtest K14 files
Jtest averages for selected populations
EUtest K13 files
EUtest averages for selected populations
The Jtest folder contains files that can be used to make an Ashkenazi ancestry test/chromosome painting with 14 Eurasian and African clusters. The EUtest folder contains the same files, except that the Ashkenazi allele frequencies have been removed. It’s useful to cross check results from both tests, mainly to see what’s hiding under the Ashkenazi admixture if it shows up in the Jtest.
Based on a few test runs today, I’d say that the noise level for the continental clusters is much less than 1%. But it rises to a few per cent for the intra-West Eurasian clusters. In other words, if you’re European, then you might score something like 0.02% in the Sub-Saharan cluster, which basically means 0%. However, you might get around 2% in the Middle Eastern cluster, even though you’re from Central Europe, and you don’t have any recent Middle Eastern ancestry. You can blame various prehistoric and historic migrations into Europe for these seemingly quirky results, and also the fact that Mesolithic Europeans were significantly Eurasian (i.e. Siberian, Amerindian and South Asian-like).
The Ashkenazi cluster is very similar to the Middle Eastern cluster in that regard. So anyone who gets an Ashkenazi score of around 2-3% either has very distant Jewish ancestry or, more likely, none at all. However, those who show more than 25% membership in that cluster are almost certainly of fully Ashkenazi ancestry, and their genomes peppered with Ashkenazi-specific chromosomal segments.
Wow, there’s really not much difference between 2% and 25%, you might say. In fact, there is if we say there is. As always, the main thing to remember is that these clusters don’t really exist, because genetic variation is clinal, so the cluster names are basically arbitrary and it’s always the relative results that matter. That’s why to really understand what your scores mean, you need to compare them with those of other users.
Obviously, it's best to compare with people from the same ethnic and/or regional groups. If the Ashkenazi + East Med scores look relatively inflated, that's a sign of recent Ashkenazi ancestry.
Feel free to use the files above for anything you want, except commercial stuff. Please note, I make no guarantees that they’ll provide accurate results for everyone. I might update this post early next week with new and/or additional files and more tips.
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Update 6/10/2012: The Jtest K14 and EUtest K13 will soon be available at GEDmatch, accompanied by an "Oracle" population matching analysis and maybe even a 3D genetic map. If all goes to plan, the population matching test should be able to give a decisive yay or nay to anyone wondering whether they have recent Ashkenazi ancestry.
By the way, below is a PCA based on the Jtest averages for selected populations. It was produced by one of my project members so that we could check the reliability of the 14 "ancestral" components. The samples were classified into clusters based on their highest peaking component. So, for instance, the Scots are in the light blue Atlantic cluster, along with French Basques, because the Atlantic component dominates in both groups. However, overall, they're more similar to other samples than to each other.
As per above, the plan is that GEDmatch will soon offer a 3D genetic map based on the loadings from this PCA analysis.
Update 11/10/2012: The Jtest and EUtest are now on offer at GEDmatch. The quickest way to get there is via this link to the Ad-Mix page. Then, from the drop down menus, choose Eurogenes, followed by Jtest.
First run the Admix test to check whether your Ashkenazi admixture is significantly higher than expected for your part of the world (as per above, Jtest averages for selected populations are available here). Then move on to the Oracle analysis by pressing the relevant button at the bottom of the page.
If your Ashkenazi admixture is clearly elevated, and the top 20 single and/or mixed mode Oracle results show AJ (Ashkenazi Jews) as one of your potential matches, then it’s likely you have recent Ashkenazi ancestry.
Whether that’s the case or not, you can then move on to the Chromosome Painting feature to see where the potential Ashkenazi admixture is located in your genome. It’s useful to cross check the results with those from the Ancestry Finder at 23andMe to assess their accuracy.
As already mentioned, the EUtest is exactly the same as the Jtest, but with the Ashkenazi allele frequencies taken out. You can use this option to see what’s hiding under your Ashkenazi admixture in the Jtest. To compare your results with those of selected populations from Europe, Asia and Africa, refer to the EUtest averages sheet.
Please note: it's important to interpret the results with insight. You need to learn how the system works, pay attention to the types of populations that appear in your results, consider carefully why they might be paired with other populations, and of course study the statistics in detail. Expecting a bullseye classification at the top of the Oracle list is likely to lead to major disappointment for many people, simply because I don't have enough samples to represent all of the substructures that exist around the world, especially within countries.
I’ll try and update both tests in a few weeks, after seeing how successful the whole set up is at predicting Ashkenazi admixture and locating it in the genome. One of the main goals will be to improve the accuracy of the Oracle analysis for everyone, including New World people with Amerindian admixture.
Update 21/10/2012: Below are gradient maps of a few of the ancestral clusters from the Jtest, courtesy of project member FR7.
Update 4/12/2012: 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.
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).
