Part 1 - Admixture Proportions

Introduction

Despite all the help articles available on Gedmatch, 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. In fact, there is a very good beginners guide to the matching side of things found here: http://smithplanet.com/stuff/gedmatch.htm. 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: https://www.gedmatch.com/gedwiki/index.php?title=Admixture - and there is Kitty Cooper's slide presentation: http://slides.com/kittycooper/gedmatch#/ - but I don’t think they really answer all the questions most people are looking for, especially regarding Oracle.  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

Eurogenes

Dodecad

HarappaWorld

Ethiohelix

puntDNAL

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.

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

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. There is a third button which just says "Spreadsheet" but there is a good explanation for this from Roots & Recombinant DNA so there's no need for me to go over it: http://www.rootsandrecombinantdna.com/2015/12/gedmatchs-new-spreadsheet-feature.html 

Oracle

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

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.

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.