Genetics basics for people that don't know anything about it [part 3]๐งต
![Genetics basics for people that don't know anything about it [part 3]๐งต https://t.co/lQ0v4KQiF0](https://pbs.twimg.com/media/FTUEwsWXsAAz1SV.jpg)
This will be the final part of the Genetics basics series. Here we will look at a hypothetical person that did a dna test and wants to know more about it, we will look at a modern population composition and we will examine an ancient group.
Our hypothetical person is Italian that got his dna results back where he finds out that he has a paternal haplogroup R-U152 and a maternal haplogroup H1e1. He sent his DNA file to Illustrative DNA and got his coordinates back.
First we will look at his paternal haplogroup R-U152. First we will keep it simple going to google and then check out what wikipedia has.
Here we see that R-M269 is a sub-clade of R1b and that R-U152 is a sub-clade of R-M269 (remember the tree and branches analogy).
We can see some information about R-U152 here with papers being cited. We can use these references to look up the papers and read them ourselves.
We can see some information about R-U152 here with papers being cited. We can use these references to look up the papers and read them ourselves.
First we will look at the Myres et al study to learn more about its modern presence. First we scan the visual data. We can see M269 frequencies being given but no specifically U152. So we move on to the next paper.
This paper is behind a paywall so we copy the doi url and go to sci-hub.se posting it there to download the paper. Scanning the paper we notice U152 being called R1b1b2h. here. We'll look over the visual data again. We can see a map with frequencies given and a table
Now we have a decent idea of the modern distribution of R-U152. We didn't look up more papers or look into the paper in detail to check its methodology and the authors' comments, but this is enough for the basics.
Next up we will look what ancient dna of U152 has been found. Again we will keep it simple and look at the citations given on wikipedia.
The first one doesn't mention U152 only M269 neither does it in its supplementary materials. The second paper gives us nothing.
The first one doesn't mention U152 only M269 neither does it in its supplementary materials. The second paper gives us nothing.
The last one doesn't give us a sample of U152 and it is not clear which group it belongs to or what time frame. The study is about a large area a long time span and involves various groups.
We didn't learn much from this. A good lesson that wikipedia can be useful but it is not without flaws. We use google scholar to look up more papers. After a bit of looking we find a paper talking about U152 and it being unclear at publication date (2014) where its origins are.
After looking a bit more we finally find something worthwhile. This is after the study from the tweet above it has an ancient dna analysis reference which we were looking for and it is from a recent study (2021). Absolutely perfect to draw conclusions from.
From this we can conclude that U152 has not only probably been among the Etruscans but even among Villabruna individuals.
The same process is how you look up the maternal haplogroup. I am not going to do that. So lets just assume it is just as old and from the same place as U152. Now we are going to use G25 (Vahaduo) to see the autosomal composition of the individual (see part 2 for how)
The right way to approach this is to look up studies about the autosomal composition of Italy see what ancient populations it consists of and then use those populations in the source tab. Then add the the population sources Davidski's basic model uses (see part 2)
The best way to look up papers regarding this is to use terms like "autosomal Italy qpAdm" or "autosomal Italy admixture". You can add the term ancient dna if the other terms don't work. I'm just going to use this study that's about Europe in general. LBK is Early European Farmer
Davidski's model already has everything from the qpAdm above so we will just use that. After the first run we get a nice result with great a distance. Remove the source populations with less than 5%. This gives a false signal of Levant PPNB remove that too. Finally we are done
Now we have the autosomal composition and the origins of and modern distribution of R-U152 (mtdna if we had done that too). A good thing to do would be to do an autosomal analysis of older Italian populations so ancient Romans, Etruscans, medieval dna etc. And to compare it.
We can conclude that our hypothetical Italian is very Italian
Next up we will look at the composition of a modern population. We will look at the Netherlands. The paternal haplogroup composition was not hard to find. For the autosomal composition we are just going to use the same Davidski model as earlier.
The distance in our G25 is not bad but it is not great either. The best thing to do now is to add more samples from the 3 same populations to see what happens (eurogenes gives both the average of samples and all non averages. We need the latter one here).
To not leave it open ended I have my own model that works on most if not all populations world wide. It is beyond the scope of this thread how I made it. These are the results:
Now we will look at an ancient group to check their DNA. We will look at the Bell Beaker culture.
A study from 2018 shows us that outside of Iberia most had R1b-M269. We will now look at the autosomal composition. A study gives an admixture analysis and a PCA. From the admixture analysis we can see that Belll Beakers besides in Iberia have a lot of steppe DNA
You can see that Steppe is very simplisticly said red and green and Bell Beakers have the same composition plus some blue. The blue probably comes from Early European Farmers. The other options is Levant neolithic but we can see in the PCA Bell beakers cluster differently.
From the paper about the autosomal composition we can conclude that we can just use the Davidski model. This gives us great results. Now you know the genetic make up of the Bell Beaker people.
[END]
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