Comparing your autosomal genetics with ancient populations

Stefanthro

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Ethnic group
Bosnian Serb
Y-DNA haplogroup
J2b2>L283>J-Z38299
mtDNA haplogroup
H4
Hi everyone,

I'm a long-time lurker. I've always been fascinated with genetics, and have focused on haplogroups a bit more than autosomal DNA because I always thought the latter was kind of inaccessible to a layman (I'm an anthropologist, but not a geneticist). On this site I'm constantly seeing people posting comparisons of ancient populations' and specimens' autosomal DNA to one's own... Can anyone point me in the right direction for where I can learn to do this myself? Do I need a specific tool or software? Do I need a particular DNA test in order to have the right raw data? (I have 23andme only at the moment.) Where can I find data on the ancient populations I'm looking for (ex. specific specimens, or data on WHG, EEF, etc.)? I'm not even sure where to get started!

Thanks in advance.
 
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Hi everyone,
I'm a long-time lurker. I've always been fascinated with genetics, and have focused on haplogroups a bit more than autosomal DNA because I always thought the latter was kind of inaccessible to a layman (I'm an anthropologist, but not a geneticist). On this site I'm constantly seeing people posting comparisons of ancient populations' and specimens' autosomal DNA to one's own... Can anyone point me in the right direction for where I can learn to do this myself? Do I need a specific tool or software? Do I need a particular DNA test in order to have the right raw data? (I have 23andme only at the moment.) Where can I find data on the ancient populations I'm looking for (ex. specific specimens, or data on WHG, EEF, etc.)? I'm not even sure where to get started!

Thanks in advance.


Hey there.

1.First you need an autosomal test. 23andme has autosomal tests iirc, if you have done the autsomoal test then you need
2.Calculators. Either download admixture studio (I highly recommend as it has most calculators, also get pro for 12$ I think its worth it if not only for the visualisation tools), or use vahaduo. (https://dnagenics.com/admixture-studio/) (http://vahaduo.genetics.ovh/)
3. There is an option to obtain G25 coordinates and play around with the G25 calculators I find better than traditional K13 or K12 calculators. But again getting the G25 coordinates costs around $15.

Let me know if you have the autosomal results. Then I can help you out with using admix studio or vahaduo. G25 is optional and a luxury IMO.

PS: Are you an anthropologists by profession or hobby?
You are the second guy I see with J2b2 (L283) on this forum and a Canadian flag, seems Canada is a magnet for our Haplogroup.
 
Hey there.

1.First you need an autosomal test. 23andme has autosomal tests iirc, if you have done the autsomoal test then you need
2.Calculators. Either download admixture studio (I highly recommend as it has most calculators, also get pro for 12$ I think its worth it if not only for the visualisation tools), or use vahaduo.
3. There is an option to obtain G25 coordinates and play around with the G25 calculators I find better than traditional K13 or K12 calculators. But again getting the G25 coordinates costs around $15.

Let me know if you have the autosomal results. Then I can help you out with using admix studio or vahaduo. G25 is optional and a luxury IMO.

PS: Are you an anthropologists by profession or hobby?
You are the second guy I see with J2b2 (L283) on this forum and a Canadian flag, seems Canada is a magnet for our Haplogroup.

Thanks for the response!

1. I do have an autosomal test with 23 and me!
2. Ok, this is great to know. Unfortunately I have a mac, and it looks like this is for PC only :( It looks like I'll have to find a mac-friendly software, or get windows. Let me know if you (or anyone else reading those) knows of something!
3. I'm assuming these are databases with particular datasets and formulas? (Sorry, I'm a total newb lol)

Appreciate your help!

I guess I'm technically a hobby anthropologist - I have 2 degrees, but I'm applying my cultural-anth skills in business to do market research - so not professionally employed as an anthro. I focused a lot of human evolution in my program, worked in archaeology for a few years, and then went back to get cultural-anth training to make a career pivot.

Cool, looks like we're probably the same group! I haven't done the big Y-700 yet, so I don't know if I'm L283 (23andMe didn't say I was), but I hope to discover more when I build up the nerves to spend that much on a genetic test. My paternal lineage comes from the Montenegrin coast, and the story goes that they fled there from Hercegovina when the Ottomans attacked. It looks like we're neighbours - are you from Albania proper or the surrounding area?
 
Thanks for the response!

1. I do have an autosomal test with 23 and me!
2. Ok, this is great to know. Unfortunately I have a mac, and it looks like this is for PC only :( It looks like I'll have to find a mac-friendly software, or get windows. Let me know if you (or anyone else reading those) knows of something!
3. I'm assuming these are databases with particular datasets and formulas? (Sorry, I'm a total newb lol)

Appreciate your help!

I guess I'm technically a hobby anthropologist - I have 2 degrees, but I'm applying my cultural-anth skills in business to do market research - so not professionally employed as an anthro. I focused a lot of human evolution in my program, worked in archaeology for a few years, and then went back to get cultural-anth training to make a career pivot.

Cool, looks like we're probably the same group! I haven't done the big Y-700 yet, so I don't know if I'm L283 (23andMe didn't say I was), but I hope to discover more when I build up the nerves to spend that much on a genetic test. My paternal lineage comes from the Montenegrin coast, and the story goes that they fled there from Hercegovina when the Ottomans attacked. It looks like we're neighbours - are you from Albania proper or the surrounding area?

I would be willing to help run your coordinates, but I will be going on vacation tonight, and wont bring my laptop, plus for the sake of privacy I would rather not handle your raw data. So my advice is install windows if you can or some emulator?

The G25, are basically coordinates derived from your raw data, which you can use in G25 calculators, and from my experience they are the better calculators.

I am an Albanian from N. Macedonia.

Also, since you are J2B2, 99% you are L283. Since 100% of European J2B2 is L283. The other branch of J2B2 is in India.

The two branches split 9500 years ago.
https://www.yfull.com/tree/J-M241/

J2b-M102-Project-2009_edit-2015.png


You can read more what I think about L283 and some of the current facts and the consensus here:

https://www.eupedia.com/forum/threads/41455-Current-J2b2-L283-Evidence-A-speculative-Theory
 
I would be willing to help run your coordinates, but I will be going on vacation tonight, and wont bring my laptop, plus for the sake of privacy I would rather not handle your raw data. So my advice is install windows if you can or some emulator?

The G25, are basically coordinates derived from your raw data, which you can use in G25 calculators, and from my experience they are the better calculators.

I am an Albanian from N. Macedonia.

Also, since you are J2B2, 99% you are L283. Since 100% of European J2B2 is L283. The other branch of J2B2 is in India.

The two branches split 9500 years ago.



You can read more what I think about L283 and some of the current facts and the consensus here:

That's awfully kind of you - please enjoy your vacation! I also feel weird about sharing it - it's best if I learn from the expertise of people like yourself :)

I did see that and assumed that would be the case too - I read the J2 article that explained 99% of European J2s are L283 and Z628 (can't send links until I hit 20 posts apparently). 23andme did also say I have trace amounts of South Asian ancestry, so maybe it's possible - but I assume highly unlikely it's not the European / Balkan variant.

Great, I will try to get an emulator going and will follow up (it will probably take me a few weeks). Thanks again for your help so far, I may return to this thread to poke you or any others again.
 
Gedmatch needs to add more calculators focusing on Ancient DNA.
 
Hey again Archetype0ne,

It's been a long time but I finally got a windows machine and bough Admixture Studio! I ran a few calculators and have been enjoying seeing results (although I want to find a bit more about the sample populations of a few groups in some of the calcs).

I also wanted to get the G25 calculators but I accidentally bought the G25 Studio lol and I'm not really sure how to use it. Was that the right thing to do, or am I supposed to find the G25 calcs within Admixture Studio?

I'm also really hoping there's a calc out there that can tell me proportions of the big 3 European populations - EF, WHG, Yamnaya. I found a few that have similar results, like WHG, EHG, and Anatolian Farmers (not sure of that's considered EF or ancestral to it, or if it's a separate group), but not quite certain it's what I'm looking for.

Let me know if you're able to provide any info on the above, or if you know where I can find some more tutorials or something to learn more about how to use this software / about analyzing genetics in this way. Thank you!
 
Nice to hear you are enjoying playing around with the calcs.

G25 studio up to some time ago was not what you needed, but since vahaduo G25 is currently down due to some intellectual property issues from what I can tell, it might still come in handy. The fact remains though that you will need the G25 coordinates to play with it.

Can't recall if Admixture studio has what you are looking for, but IIRC not exactly, why I found G25 so useful since it had a curated list of samples (albeit sometimes misnomered) which one could use to make custom models.
Sadly the samples were taken down https://vahaduo.github.io/vahaduo/, can't recall the details but something about open source ip being used to advertise add ons or what not.... So the G25 calc you bought comes in quite handy here.

From what I see Davidski discontinued the G25 coordinates service for the time being: https://bga101.blogspot.com/2021/08/genetic-ancestry-online-store.html

Seems July 2022 is when the service will be available again.

Technically though, you could run a WHG, EHG, EEF model in an other way. But have not done it myself so don't want to mislead you.
You would have to find the (say for example K13 calc, or K12b) coordinates for the representative samples, them being coordinates for WHG, EEF and EHG, then play around with vahaduo vis a vis your own K13 coordinates here https://vahaduo.github.io/vahaduo/.
You would put the EHG, WHG, EEF, or any other model you want to analyzed in the source tab, and your own coordinates on the target tab.

As far as finding coordinates for EHG, WHG, EEF etc, I am not the best person to ask there are far more knowledgeable people on this, maybe try Jovialis a moderator here, or Salento who I see posts coordinates quite often.

Hopefully this helps.
 
It seems this problem has come up before and luckily Salento did indeed save the coordinates for the models:

here it is, ... the archived data of the site with some extra samples here and there.
… fyi, it included tons of coordinates processed by Jovialis, also contributions by Maciamo, Duarte, others, … and me :)

… the App with the 2WAY is included.

https://www.mediafire.com/file/qc77mbcfldkbr1l/dna_data_and_oracle.zip/file


You would fetch the coordinates for either K12B or K13, find among them samples that might be representative for the populations you are looking for, and build models that way.
 
Thanks so much for your help with this! Did not know how to navigate this DIY world and I really appreciate your telling me where I can get some shoes to learn to walk lol.

All the best
 

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