Thursday, April 6, 2017

Finally! A Gedmatch Admixture Guide!

For those unaware, Gedmatch.com is a website where you can upload your raw DNA data for further analysis and matching with people from other companies who have also upload their data.

This guide is also available from Google Docs.

Part 1 - Admixture Proportions

Introduction
Despite all the help articles available on Gedmatch.com, none of them really offer a comprehensive guide to understand the admixture calculators for newbies. Most of them are guides on understanding DNA in general, or how to upload your data, or using the one-to-many or one-to-one tools. But the most common questions I see about Gedmatch are “which admixture calculator do I use?” and “what do the results mean?” There is a Gedmatch wiki page on admixture found here: https://www.gedmatch.com/gedwiki/index.php?title=Admixture - but I don’t think it really answers the questions most people are looking for. Even Googling the topic only turns up spotty results from forums and blogs, nothing that really lays it all out. Since no one else has done it, here is my attempt. Please keep in mind I am no expert and have no formal education in genetics, this is just the knowledge I’ve gathered over the years from various sources as a result of trying to understand my own DNA results.

Admixture is a scientific term for the ethnicity percentages you received from a DNA company like Ancestry.com, FamilyTreeDNA, 23andMe, or MyHeritage. It’s important to understand that each admixture project on Gedmatch is created by a different person, mostly academics. Note that most of the admixture results will include some basic info on the calculator, either on the results page, or through a link from the creator. However, the info provided may still be technical and difficult to understand for the average person, because they were primarily created for academic purposes. This is an attempt to translate some of that info into something more understandable to the average user. I apologize that this guide favors info on European backgrounds, but that is simply what I’m most familiar with, being a European descendant myself.

Be aware that it’s common practice in DNA admixtures to refer to populations from prehistoric times as “ancient”, even though this is a bit of a misnomer. In historical terms, ancient history marks the beginning of recorded history, but here, “ancient” generally refers to the time before written history, prehistory. Some time periods might be specified as “neolithic”, or “paleo/paleolithic”.

Step 1: Pick a project.
(Below the projects drop down menu there are options like "Admixture Proportions (with link to Oracle)" and "Chromosome Painting", etc. Don't mess with those for now, just stick with the top default option, Admixture Proportions (with link to Oracle), as that is what this guide will cover.)

There are 7 projects to choose from, but what are they? What do they mean? Which one should you pick? Here’s a basic breakdown:

  1. MDLP
This is a global calculator and attempts to break your results down into different parts of the world. It’s good as an overview, but if, for example, you already know you’re European, it’s probably unnecessary. It’s also heavy on ancient groups. The blog for this project is found here: http://magnusducatus.blogspot.com/

  1. Eurogenes
As the name suggests, this is primarily for people with European backgrounds. While it does have populations outside Europe, there are usually more sub-continental regions for Europe than any other continent. I highly recommend this as the go-to project for people with sole European ancestry. The blog for this project is found here: http://bga101.blogspot.com.au/

  1. Dodecad
This project says it focuses primarily on Eurasians, but most of the calculators are geared more towards Asian and African ancestry than European. It’s not ideal for Europeans, but may be useful for people with mixed ancestry. The blog for this project can be found here: http://dodecad.blogspot.com/

  1. HarappaWorld
This calculator is primarily for people with Asian ancestry. The blog for this project can be found here: http://www.harappadna.org/

  1. Ethiohelix
This is an African based project, though it does have options for people with mixed backgrounds (but always including African). The blog for this project is found here: http://ethiohelix.blogspot.com/

  1. puntDNAL
This is primarily a project on ancient DNA. There is no website, but questions and comments about should be directed to Abdullahi Warsame at puntdnalking@gmail.com

  1. GedrosiaDNA
This project focuses primarily Eurasian (especially Indian and Asian) and ancient DNA. There is no website, but for further questions, please contact the creator at Dilawerkh4@gmail.com

Step 2: Pick a calculator.
You’ll find that for each project, there are often several calculators to choose from. How to choose? What do they mean? What are the differences? Well, for starters, the numbers following a ‘K’ indicate how many populations (or regions/categories) that calculator includes. So for example, Eurogenes EUtest V2 K15 has 15 populations. So choose one depending how many regions you want to break your results down into. Keep in mind the more populations and therefore the more specific the regions are, the more speculative the results will be.

Certain other tests may be specific to deeper, more ancient (prehistoric) ancestry, like Hunter-Gatherer vs Farmer. Any abbreviation that starts with ‘A’ probably stands for ‘ancient’, but I will post a comprehensive terminology list at the end of this guide. These calculators for ancient DNA aren’t very useful if you’re just looking for an opinion on your more recent ethnicity results.

Other calculators might be specific to certain types of ancestry. For example, Eurogenes’ Jtest is specific to Ashkenazi Jewish ancestry. There’s no need to run this test if you don’t have any Jewish ancestry. In fact, you might get false results in Ashkenazi if you run this calculator and have no Jewish ancestry.

Here’s a more detailed breakdown of each calculator.

MDLP
  • MDLP K11 Modern - 11 global populations including ancient
  • MDLP K16 Modern - 16 global populations including ancient and modern, results page includes full population descriptions
  • MDLP K23b - 23 global populations including ancient
  • MDLP World22 - 22 global populations including ancient, full details including maps of what areas each category covers are found here: http://magnusducatus.blogspot.com/2012/09/behind-curtains-mdlp-world-22-showcase.html
  • MDLP World - 12 global populations, probably the original MDLP calculator

Eurogenes

Dodecad

HarappaWorld
  • HarappaWorld only has one calculator and as explained above, it’s primarily for Asian ancestry. It does include some European, African, and Native American populations, but it has more break down for Asia and the Middle East.

Ethiohelix

puntDNAL
  • puntDNAL K10 Ancient - 10 ancient populations, incorporates Caucasus HG as well as Early Neolithic Farmers and Western European HG.
  • puntDNAL K12 Ancient - 12 populations, utilizing ancient oracle, more info provided on results page
  • puntDNAL K12 Modern - 12 populations utilizing modern oracle, more info provided on results page
  • puntDNAL K15 - 15 populations, focuses primarily on Africa (particularly East Africa), but also includes some West Asia, and Europe. More info: https://www.gedmatch.com/gedwiki/index.php?title=Admixture_Calculators#PuntDNAL_K15_-_African_Ancestry_Calculator
  • puntDNAL K8 African only - 8 populations, as the name suggest, it’s strictly an African calculator

GedrosiaDNA

Step 3: Understanding the results: A Terminology Guide
A list of populations you might see and a brief description. I did not include some of the most self-explanatory ones. Some that I have listed might still be obvious to some people, but I’ve seen others ask about them on occasion. If there isn’t one listed here, you might learn a lot by just googling it. There is also a good abbreviation guide here: https://isogg.org/wiki/Abbreviations
Keep in mind different calculators may use different terms to refer to the same region or population.

  • Amerindian or Amerind - Native American (ie, American Indian meshed into one word)
  • Anatolian - mostly Turkey
  • Ancestral Altaic - Asia (excluding South), and Eastern Europe
  • ANE - Ancient North Eurasian
  • Archaic African - broad category for prehistoric Africans
  • Archaic Human - broad category for prehistoric humans around 500,000 years ago
  • ASE - Ancient/Ancestral South Eurasian
  • Ashkenazi - Ashkenazi Jewish of central/eastern Europe (not the same as Sephardic Jewish)
  • ASI - Ancient/Ancestral South Indian
  • Australian - aboriginals of Australia
  • Australoid - “people indigenous to Southeast Asia, South Asia, Australia, Melanesia, Polynesia, Micronesia, and historically parts of East Asia.” (Wikipedia)
  • Austronesian - “relating to or denoting a family of languages spoken in an area extending from Madagascar in the west to the Pacific islands in the east.” (Google)
  • Baloch - people of Iranian Plateau and Arabian Peninsula (primarily the Middle East)
  • Baltic - regions surrounding the Baltic sea
  • Bantu - Central and south Africa
  • Basal - Basal Eurasian?
  • Beringian - areas surround the Bering Strait (Eastern Russia and Alaska)
  • Biaka - aka Aka, “nomadic Mbenga pygmy people who live in southwestern Central African Republic and the Brazzaville region of the Republic of the Congo” (Wikipedia)
  • Caucasian/Caucasus - people of the Caucasus region, the border between Europe and Asia in between the Black sea and the Caspian Sea
  • CHG - Caucuses Hunter Gatherers
  • EHG - Eastern Hunter-Gatherer
  • ENF - Early Neolithic Farmer
  • Fennoscandian - Scandinavia and Finland
  • Gedrosia - Modern day Makran (semi-desert coastal strip in Balochistan, in Pakistan and Iran, along the coast of the Persian Gulf and the Gulf of Oman)
  • Khoisan - Southern Africa
  • Mbuti - “one of several indigenous pygmy groups in the Congo region of Africa” (Wikipedia)
  • Melanesian - “a subregion of Oceania (and occasionally Australasia) extending from the western end of the Pacific Ocean to the Arafura Sea, and eastward to Fiji.” (Wikipedia)
  • Mesoamerican - Native American in Mexico, Central and South America
  • NAF - Neolithic Anatolian Farmer
  • Oceanian - Aboriginals of the Pacific Ocean islands (may include Australia depending on calculator)
  • Omotic - Southwest Ethiopia
  • Papuan - New Guinea and surrounding islands
  • Pastoralist - Sheep or cattle farmer
  • Pygmy - “certain peoples of very short stature in equatorial Africa and parts of Southeast Asia.” (Google)
  • San - Bushmen of southern Africa
  • SEA - South East Asian
  • SSA - Sub-Saharan African
  • Steppe - “ancient North Eurasian hunter-gatherers' heritage, which was subsequently shown to have an influence in later eastern hunter-gatherers and to have spread into Europe via an incursion of Steppe herders” (MDLP K16)
  • Tungus-Altaic - Northeast China and Siberia
  • WHG - Western Hunter-Gatherer
  • WHG-UHG - Western Hunter-Gatherer/Unknown Hunter-Gatherer
  • Volga-Ural - Part of Russia (central)

Conclusion
Which project and calculator you go with greatly depends on your known ancestry. I know all this info is probably still a little overwhelming even with (or perhaps because of!) this guide. If you’re of European descent, and a newcomer to Gedmatch, and you just want a second opinion on your ethnicity results from any of the Big 3 companies (Big 4 now maybe, with MyHeritage joining the bandwagon), I’d recommend Eurogenes K13 or K15. Personally, I tend to prefer K15, because there are maps available showing specifically what regions are covered by which populations. Certainly, you can play around with any of the other Eurogenes calculators too (except Jtest if you’re not Jewish). Most of the other projects and calculators are either geared more towards ancient DNA, other continents, or a mixed ancestry. You may find a non-bias global calculator in some of the other projects, but it’s probably not going to provide the breakdown of Europe you’re looking for.

If you’re looking for an ancient calculator, I again tend to stick to one of Eurogenes’ (HG vs F, or ANE), but MDLP have some good options too. There’s also a couple in puntDNAL which I don’t think have a bias towards any one type of ancestry.

If you’re African, Asian, or of mixed heritage, there are a number of options to choose from, but I unfortunately can’t recommend any over any others. Most global calculators will include Amerindian (I have tried to note when a global one doesn’t).

It is frustrating that maps, or at least population descriptions, aren’t available for every calculator, but this is a free service, after all. It’s actually pretty amazing all the work the project creators do to provide this for free.



Part 2 - Oracle
Say what now?

Introduction
The second most common questions I see about Gedmatch are about Oracle. What is it? What do the results means? Oracle is an attempt to pinpoint your origins to a more specific population or region. There are two options: Oracle and Oracle 4. You will find buttons for them listed under your admixture results. Note that not all admixture calculators have Oracle available.

Oracle
Oracle will list your admixture results, then something called Single Population sharing, and finally Mixed Mode Population Sharing.

  • Single Population Sharing attempts to pinpoint a specific, single population that your DNA most closely matches, with a list of the top 20. The distance will tell you how closely you match each group, so the smaller the distance number is, the more closely you match.
  • Mixed Mode Population Sharing will show you your top 20 of two specific, combined populations in order of how closely you match those populations. Again, the distance will tell you how closely you match this combo of populations, while the percentage will tell you how much of your DNA matched which population.

Oracle 4
Oracle 4 is essentially the same as Oracle, except it expands on it by providing combinations of 3 and 4 specific populations. The single and double combinations can be different from original Oracle though, so don’t bypass Oracle thinking you’ll get that and more with Oracle 4, it’s best to examine both.

  • Using 1 population approximation works the same as Single Population Sharing in Oracle, but I’ve noticed the results are sometimes different, so they’re obviously using a slightly different calculation. Reading the results works the same though: they are showing you a list of specific populations you most closely match, with the distant showing you just how closely you match.
  • Using 2 population approximation also works the same as Mixed Mode Population Sharing but again, results may vary, and for some reason only lists your top 1 result instead of the top 20.
  • Using 3 population approximation works the same as 2, but with a combination of 3 populations instead. One result.
  • Using 4 population approximation obviously uses a combination of 4 specific populations you most closely match and lists your top 20 combos. This was designed especially for people who have 4 grandparents from 4 different places. It can also work well if most of your ancestry is mainly from 4 different places.

Conclusion
Be aware that the results from Oracle and Oracle 4 will vary depending on what admixture calculator you used, which is why they are found on the admixture results page, and not as a separate calculator. Also keep in mind the results are speculative, but I have found they do often make some sense, and in some cases, can be remarkably accurate.

15 comments:

  1. Excellent information. Thank you!

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  2. This is really useful and needed. Thank you! Great work.

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  3. I have always found Gedmatch's admixture very confusing. The information you have shared has cleared it up. Thank you for your excellent article.

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  4. Thank you. Lots of information to filter. However, I'm so gratefully you shared this awesome knowledge.

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  5. Great. Any info on chromosome painting?

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    1. I might do another guide on the other options by Admixture by chromosome and Chromosome painting if it seems like there's a demand for that.

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  6. Very useful! Thank you very much.

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  7. Hello, your information is quite helpful. I was wondering, if you have a key for some of the place listed as 2 letter abbreviations when you look at the Oracles? I can guess on some and others leave wondering where they are referencing. Here are some examples that I just do not known: Hu, PT, ES, RO, and IE. Thanks for your information in the blog post.

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    1. That's interesting, I don't think I've ever come across two letter abbreviations in Oracle - you must match some populations I don't. Which calculator are you using when you get these results?

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    2. I think I figured it out... It is European country abbreviations. Silly, I finally put the right key words into google https://mfi-assets.ecb.int/resultMfiD/abbreviations Thanks again for your information.

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  8. This comment has been removed by a blog administrator.

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  9. Excellent article. Do you know what to do on the Oracle if the single population is totally different from the four population estimate? Do you pick the one with the lower number or the one that is a better fit to your known history? Also, I had several ZERO diatances. Is that good? Thank you for any help you can provide. I've been scouring the Internet.

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    1. Zero distance from a population on Oracle would mean you matched that population exactly, so that's very good. I don't think there is ever a definitive answer though, since this is all very speculative data. I would take it all into consideration.

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  10. Excellent article. Do you know what to do on the Oracle if the single population is totally different from the four population estimate? Do you pick the one with the lower number or the one that is a better fit to your known history? Also, I had several ZERO diatances. Is that good? Thank you for any help you can provide. I've been scouring the Internet.

    ReplyDelete