Sunday, September 17, 2017
I've had a few requests from personal genomics customers to stick their files into an Identity-by-Descent/cM matrix like the one at the link below. Also please check out the accompanying comments thread for ideas of what can be done with the output. A Bronze Age dominion from the Atlantic to the Altai I can do this for $15 (USD) per individual.
Please e-mail the data and money (via PayPal) to eurogenesblog [at] gmail [dot] com. The deadline for sending through the data files (which, in this run, can only be from 23andMe, Ancestry or FTDNA) is this time Tuesday.
I'll send out the results to each participant over e-mail. However, participants are encouraged to post their results in the comments thread at my other blog here, so that they can be discussed and analyzed further.
Update 20/09/2017: The analysis is underway. Please don't send any more data files. If there's enough interest, I'll do another run soon.
Update 22/09/2017: I've just sent out the results to the participants in the form of two text files titled "ancients_only" and "full_column". The former is a matrix of overall shared haplotype tracts in centimorgans (cM) that includes the user and 65 ancient genomes, and the latter a list of haplotype tracts, also in cM, shared between the user and well over 3000 public samples.
So what can we do with these files? For one, we can look at them, because simply eyeballing these sorts of stats can be very informative. Sorting the data in some way and calculating population averages might help with that.
The "ancients_only" file can be used for slightly more advanced analyses. For instance, below is a Neighbor joining graph produced with the Past 3 program (freely available here). I simply loaded my "ancients_only" file into Past 3, selected all of the columns and rows, and then did this: Multivariate > Clustering > Neighbor joining. Note that I cluster on the same branch as Slav_Bohemia, and this makes perfect sense considering my Polish ancestry. By the way, I dropped Oetzi from this run because he was behaving strangely, which is not unusual for low coverage genomes. Click on the image and open in a new tab for a better view.
here and combined, in part or in whole, with your other files so that you can analyze yourself alongside a larger number of individuals.
Sunday, September 10, 2017
This is the first of a series of guides to modeling your ancient ancestry with the Global 10/nMonte2 method. I do already have a user guide for running Global 10 and Basal-rich K7 data with nMonte and 4Mix (see here). However, in this series I’m going to recommend specific models that produce results similar to those from my experiments with other methods, such as qpAdm, as well as from scientific literature. Hopefully, this will help users achieve more sensible and accurate outcomes, and avoid problems such as overfitting. Let’s start with models for modern-day Europeans that focus on Yamnaya-related ancestry, which very likely represents a genetic signal of early Indo-European dispersals during the Early to Middle Bronze Age from the Pontic-Caspian steppe. It’s now clear via a wide range of methods that about half of the genomes of modern-day Eastern and Northern Europeans, and up to about a quarter of the genomes of modern-day Southern Europeans, are derived from such Yamnaya-related sources. Any tests dealing with ancient European substructures that don’t, one way or another, reflect this robust inference must be considered inadequate. So if my models are to be useful, then this is what they must show. And indeed they do. Here are a few examples focusing on modern-day and ancient England, in chronological order:
England_Iron_Age Yamnaya_Samara 49.75 Barcin_N 32.3 Hungary_HG 17.95 distance%=0.5318 / distance=0.005318 England_Roman Yamnaya_Samara 45.65 Barcin_N 33.35 Hungary_HG 21 distance%=0.4668 / distance=0.004668 England_Anglo-Saxon Yamnaya_Samara 44.95 Barcin_N 31.6 Hungary_HG 23.45 distance%=0.5409 / distance=0.005409 English_Cornwall Yamnaya_Samara 44.55 Barcin_N 36.95 Hungary_HG 18.5 distance%=0.3699 / distance=0.003699 English_Kent Yamnaya_Samara 45.2 Barcin_N 36.85 Hungary_HG 17.95 distance%=0.4875 / distance=0.004875The full output is available in a zip folder HERE. I’m not claiming that these ancestry proportions are perfect, especially for Southern Europeans, who generally have very complex ancestry, but they do make a lot of sense. One obvious problem with the Global 10 is that some of its dimensions, or PCs, exaggerate affinity between modern-day and Mesolithic Europeans. This is especially true for PC6. Hence, to try and mitigate this problem I decided to remove PC6 from the Global 10 datasheet used in my analysis. To try these models on your own genome, remove PC6 from your Global 10 coordinates file, and use the data text files provided in the zip folder linked to above. It’s best to rely on the datasheets specifically designed for your ethnic group or region of Europe. But feel free to tweak my models. There’s no harm in experimenting if you’re cautious and sensible about it. Indeed, using Iberia_HG or Loschbour along with Hungary_HG appears to produce more accurate outcomes for many Western Europeans. The important, but often neglected, point to keep in mind is that I designed the Global 10 to help replicate results from more reliable but technically less accessible methods, and not to challenge any generally accepted models. In the near future, a wider choice of ancient samples should enable me to fine tune and improve the models. For instance, a slightly more eastern-shifted forager reference population than Hungary_HG, such as the yet to be published Lithuanian Narva samples (see here), will probably shift the results slightly for Northeast Europeans, perhaps by bringing down their Yamnaya-related ancestry proportions by a few per cent. Moreover, adding a wide range of yet to be published Middle to Late Neolithic European samples, such as those from the Globular Amphora Culture (GAC), should prove an interesting exercise. Please note that the discussion pertaining to this post is at my other blog HERE. See also... Global 10: A fresh look at global genetic diversity
Thursday, August 10, 2017
I've updated the Basal-rich K7 spreadsheet and the Global 10 datasheets with a plethora of ancient individuals and populations, including Anglo-Saxons, British Celts (labeled England_IA), Minoans, Mycenaeans, Bronze Age Iberians and many more. The Basal-rich K7 Global 10: A fresh look at global genetic diversity An nMonte and 4mix guide for the participants of the Basal-rich K7 and/or Global 10 tests Please note that the discussion pertaining to this post is at my other blog HERE.
Monday, May 8, 2017
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/ See also... A more specific guide to modeling your genome with the Global 10/nMonte method: Your ancient ancestry #1
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.
Thursday, September 22, 2016
Judging by the Google search terms that are bringing traffic to this and my other blogs, a total newb to the scene is analyzing the Orcadian samples from the HGDP at GEDmatch with my K15 test. Please keep in mind that you will not see coherent results for many of the academic samples available online when using my tests. That's because I used these samples to source the allele frequencies for the tests. As a result, their ancestry proportions will often be very different from those of other samples from the same ethnic groups that were not used in this way. I call this problem the calculator effect, and it's described in my blog posts at the links below:
Wednesday, July 22, 2015
A few people are asking me about the effects of marker overlap or genotype rate on test accuracy. Logic dictates that the better the overlap, the more accurate the results, but this isn't strictly true. Here's what I've learned over the years:
- accuracy doesn't necessarily improve with higher marker overlap, it improves (up to a certain point) with more markersIn other words, a well designed test based on 200,000 SNPs will produce very accurate results for a genotype file with a marker overlap of 50%. On the other hand, another well designed test, based on just 50,000 SNPs, is likely to produce less accurate results for a genotype file with a marker overlap of 100%.
- you will still see accurate results using as little as 25,000 SNPs, as long as the test doesn't suffer from any serious problems
- poorly designed tests, such as those based on less than 1000 reference samples, always produce garbage results no matter what the marker overlap
So how can you tell a well designed test from a poorly designed one? It's easy, just have a look at the results they're producing for people with less complex ancestry. For instance, ask a Lithuanian, Swede or Pole what they're seeing at the top of their oracles. Is the Swede seeing Swedish or, say, German? If the answer is German instead of Swedish, or at least some type of Scandinavian, then the test is garbage and best ignored.
By the way, the recent Allentoft et al. paper on the ancient genomics of Eurasia includes a useful discussion on the effects of missing markers on the accuracy of both ADMIXTURE and PCA results. Refer to section 6.2 in the freely available supplementary info PDF here.