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Sunday, December 6, 2020

Looking forward to a post-Covid world


I was hoping that the Covid-19 pandemic wouldn't have an immediate impact on the publication of ancient DNA papers and new data, but considering how much things have slowed down in this respect, it seems that I was fooling myself.

So let's take a break until early next year, and then see what happens.

Trust me, we've got a lot to look forward to in the post-Covid-19 world. Based on what I've heard from various sources, here are some predictions about what we might see:

- the search for the Proto-Indo-European homeland will shift west to the North Pontic steppe

- on the other hand, the search for the Proto-Uralic homeland will move deep into Siberia

- the key role of the Single Grave (westernmost Corded Ware) culture in the population history of Western Europe will finally get some attention

- following on from the above, Y-haplogroup R1b-L51 will be revealed as a Single Grave marker

- the idea that the Pontic-Caspian steppe was colonized by migrants from Mesopotamia during the Bronze Age will be forgotten, and, ironically, we'll instead learn that there was a significant influx of steppe ancestry into ancient Mesopotamia

- Old Kingdom Egyptians will come out less Sub-Saharan African than present-day Egyptians.

I probably shouldn't blab everything out, so that's all you're getting from me for now. You'll just have to wait for the rest until next year, or perhaps even the year after that.

See also...


421 comments:

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Archi said...

@EastPole

I don't trust Wikipedia sources at all. And even more so everything that you publish here, you always publish only errors. Everything that is drawn on the knee on Wikipedia is ridiculous.

DragonHermit said...

@Archi

You obviously have some agenda, since your comments are completely asinine. Croatia is tiny compared to the USSR. If you can't group those together geographically, then what about Germany, France, Italy, Scandinavia, which are multiple times bigger than Croatia?

These locations all match with pre/Proto-Illyrian civilizations, and are both high in R1b-Z2103/J2b2-L283 as are modern Greeks/Albanians. They are high in Steppe/EHG ancestry, and their maternal DNA is from the Steppe.

As for Tatars, the TMRCA of 99% of L283 is only 2500 BC, while the Y-DNA you speak of is about 500 BC. Check that tree. Western/Central Russia is full of L283 clades all over from the oldest to the youngest.

Archi said...

@DragonHermit
"You obviously have some agenda, since your comments are completely asinine."

Your comment is completely asinine. You distort the data about Croatia and about Russia, you completely ignore the times, you were caught dishonest. I wrote to you that the Tatars have a completely young subclade that came recently from Europe, which does not belong to the ancients, you could not refute anything. Study the data and be honest.

"These locations all match with pre/Proto-Illyrian civilizations, and are both high in R1b-Z2103/J2b2-L283 as are modern Greeks/Albanians"

There is no need to drag Illyrians here who have nothing to do with this data.
I2 also matches R1b in Europe, but that doesn't mean anything. One habitat does not mean due to their common spread.

Copper Axe said...

Those Bell Beaker arrows pointing upwards from southern France and Iberia hurt my brain.

The Andronovo arrow is all kinds of incorrect too, their expanse was more significant than that, especially if you count deriviations such as Karasuk.

Michalis Moriopoulos said...

@David

Hey, I'm updating my Viking samples now with the new coords. I noticed you've got VK284 marked as a Langeland sample; it's actually from Sealand. Everything else looks good!

DragonHermit said...

@Archi

Tatar L283 does not come from a "recent" subclade. That subclade is from 2500 years ago, while most L283 come from 4500 years ago. And the Romanian/Moldovan border is north of the Black Sea, which matches up with this too.

You did not "catch" anything. Croatia is a tiny place compare to places like France, Germany and Poland, let alone Russia, and this was all within the Bronze Age. Saying you can't group them under "Croatia" is having a blatant agenda. Just look at the horizon of Yamnaya-like DNA.

EastPole said...

In reference to my post above about “Kalasha holidays Chaomos may come from Haoma/Soma”. Interesting article about hops:

“There are data attesting the use of hop cones, 3-5 thousand years BC, in the preparation of drinks by the Babylonians, Egyptians, etc. (Linke and Rebl, 1958). Indo-European populations used hops in brewing beer since ancient times.”

http://journals.usamvcluj.ro/index.php/hamei/article/viewFile/13981/11472

Slavs used hop cones for the preparation of mead and called it “chmiel” (=haoma/soma). So I am thinking about Herodotus reporting Budini eating fir-cones:
“The Budini are indigenous; they are nomads, and the only people in these parts that eat fir-cones”(Herodotus 4.109)
I don’t think fir-cones can be eaten, Budini probably were collecting naturally grown on fir trees hop cones for the production of mead or beer.

Archi said...

@DragonHermit

Yes, this is a recent admixture on a time scale. What has Moldova to do with it?

You are confusing the Balkans with the Steppe, for the Balkans 300 kilometers between these samples is a huge distance. This is all entirely mountains, the first sample is essentially in Hungary, the second in Bosnia or Montenegro on the sea coast, passing the state borders a little differently (5 km), you would not write about any Croatia. For you, 1200 years of difference is nothing at all, different eras and cultures do not exist for you.

Samuel Andrews said...

Video on Kievan Rus' DNA on my Youtube channel.

"Ancient DNA from Kievan Rus' shows Scandinavian admixture"
https://www.youtube.com/watch?v=jh3wxl4Feko&ab_channel=ThePopulationGeneticsChannel

I'm sure some of you have opinions on this. I definitly got some of the history wrong.

The "Viking" DNA from Russia and Poland, is really Kievan Rus DNA. And the Slavic-like Mediveal Grmans are from Kievan Rus. I think that is what Davidski was alluding to....

https://eurogenes.blogspot.com/2020/11/slavic-like-medieval-germans.html

EastPole said...

Interesting things one can find in the internet:

“There is evidence of hops cultivated by the Babylonians in 4,000 B.C. and that they prepared a drink called Sikar with it. It is also believed to be one of the ingredients in the making of Soma, a hallucinogenic drink used in a ritual way in ancient India.”

https://ibizabeercompany.com/en/beer-culture/humulus-lupulus-2/

I don’t believe hop was cultivated by the Babylonians 4,000 B.C. because hop doesn’t grow in the south. They were probably making beer using wine yeast. Most likely hop was introduced by some northern traders from Thrace or Greece much later. Scientific literature says 3000 years ago:

“Hop was used in brewing by the Sumerians and Egyptians as far back as 3000 years ago. The Babylonians and Philistines knew beer, but whether they used hops is not certain.”

https://www.sciencedirect.com/science/article/pii/B9780444881656500056

Soma was not a hallucinogenic drink. One has to be an ignorant about Rigveda and poetic metaphors related to drinking alcohol to claim such nonsense. Soma was a drink with hops, but it was most likely mead, i.e. alcoholic drink made from honey.

Drinking and religious terminology in Vedic, Thracian and Phrygian is common with Slavic, so we can conclude that Corded Ware people had similar terminology and were drinking mead and beer with hops.
The God present in the radiant sun, in the cup of mead or beer and in the hearts of Indo-Slavic men was the same god. Such was their Indo-Slavic religion which left traces in Slavic lands until recent times.

https://upload.wikimedia.org/wikipedia/commons/a/a5/Museum_f%C3%BCr_Vor-_und_Fr%C3%BChgeschichte_Berlin_031.jpg

Sam Elliott said...

You are correct that the J-Y12000 branch of J-L283 is relatively young and represents a movement from Central Europe to the east into Russia.

Sample I4331 is from the Dalmatian highlands in what is today southern Croatia. Of course this sample was not ethnically Croatian, it’s 3600 years old. Not sure why there is a resistance to referring to the sample as “Croatian”, since that’s where the Tumulus and the skeletal remains were located.

Finally, you say that J-L283 and R-Z2103 have never been found together. That is not true. The recent Mokrin paper regarding the Maros Culture burial in Mokrin, Serbia (4000 years old) had remains confirmed to belong to R-Z2103, J-L283 (specifically Z615), and I2a. Mokrin, Serbia is in northern Serbia near the border with Hungary. This is not anywhere near the coast and this is why I think L283 expanded into the Balkans from the north somewhere, perhaps from Pannonia, Hungary, or in vicinity of the Alps near Italy or eastern Austria.

Archi said...

@Sam Elliott

In Mokrin it came from the south, there can be no two opinions. Mokrin is unambiguously and without options a culture that came from the south.

I did not say that they were never in the same place, not true, I claim that their distribution has nothing to do with each other. Look at the map, the Yamnaya culture passed through this territory, so here they could coincide.

Angantyr said...

@EastPole

"I don’t think fir-cones can be eaten, Budini probably were collecting naturally grown on fir trees hop cones for the production of mead or beer."

Or...? https://www.atlasobscura.com/foods/pine-cone-preserves

Rob said...

@ East Pole

''There is a new map showing IE migrations at Wikipedia:

https://upload.wikimedia.org/wikipedia/commons/a/a6/Indo-European_expansions.jpg''

What an eye -sore

Rob said...

Mokrin cemetery

R1b-Z2103 : steppe
I2a1b- carpathian
I2a1a- Alpine
I2a2a1a- NW Europe
J2b2: looks ECE

I didn’t see a PCA or genome -wide analysis in the paper; but southern affinities seem minor & indirect

Archi said...

@DragonHermit
"Tatar L283 does not come from a "recent" subclade. That subclade is from 2500 years ago, while most L283 come from 4500 years ago."

You are deeply mistaken. You give the time of the appearance of the mutation for the time of propagation, while the time of propagation was only 1200 years ago, when it came to the Volga. And the time of appearance of the mutation is not 500BC, but 300BC, but this is one person who lived somewhere in non-eastern Europe.

You write in a strange way, for L283 you give TMRCA, and for Y12000 you give the time of occurrence of the mutation.

J-Y12000 Y12000 * Y12002 * Y12003+7 SNPs formed 2300 ybp, TMRCA 1200 ybp info

K33 said...

David I'm trying to get the AdmixTools2 Shiny web app to work, I have ANCESTRYMAP files with a greatly reduced set of pops in the IND file to test this--just 9 populations and 14 total samples. I uploaded the .ind file to the web app and the samples appear on the screen. Then I extract the.geno file and it creates folders on my disk with the "ap.rds" and "f2.rds" extensions for each pop vs each other pop. The folders with the .rds extensions are all generated within a few minutes, but Shiny_Admix did NOT generate any "block_lengths.rds" files for me.

Below is the error the R console is giving me, could you offer any advice as to what the problem is?

Warning in dir.create(outdir) :
cannot create dir '', reason 'No such file or directory'
Warning in gzfile(file, mode) :
cannot open compressed file '/block_lengths.rds', probable reason 'Permission denied'
Warning: Error in gzfile: cannot open the connection
79: gzfile
78: saveRDS
77: afs_to_f2_blocks
76: extract_f2
75: extractfun [CUsers\user\Documents\R\win-library\4.0\admixtools\shiny_admixtools/app.R#1745]
73: observeEventHandler [CUsers\user\Documents\R\win-library\4.0\admixtools\shiny_admixtools/app.R#1754]
2: shiny::runApp
1: run_shiny_admi


When I try to upload the 75MB .snp file in the Extract Settings > "SNP List" box in the shiny web app, it says "Maximum Upload size Exceeded". Not sure if that has anything to do with this.

Davidski said...

If you want the run_shiny_admixtools() function to work, and you don't have a powerful computer, try this...

Create a PLINK data file (named data) with the populations/samples of interest and generate f2 stats from it, like this...

prefix = "C:/Users/Davidski/Documents/Admixtools2/data"

my_f2_dir = "C:/Users/Davidski/Documents/Admixtools2/f2-stats"

extract_f2(prefix, my_f2_dir)

Then after calling the run_shiny_admixtools() function you'll get asked for the path to the f2 stats. This is what you must copy paste into the relevant field.

C:/Users/Davidski/Documents/Admixtools2/f2-stats

Admixtools2 will then automatically fit a graph to the observed f2-stats, and you can go from there.

Keep in mind, though, there are quite a few options available, and you have to become familiar with all of them to generate solid graphs.

K33 said...

Thanks for the advice. I don't have Linux tho wouldn't I need to convert my ancestrymap dataset to PLINK using Linux convertf function? I just feel like I'm close with the default setup but can't figure out what this error message is telling me.

I have a pretty new PC although it is a laptop. Specs:
AMD Ryzen 3 3200U 2.6Ghz dual-core/4 thread processor
16 GB RAM (although its single-channel)
64 bit Windows 10

I have two 250GB m.2 solid state drives (500 GB total). My R program was installed on the C:/ drive and the R/admixtools folder is on my C:/ drive too, but I'm trying to keep all the dataset files, f2 stats, etc, on the D:/ drive as I just wiped clean it for this purpose. Is that problematic-- do I *have* to use the C/Admixtools/data folder for the f2 directory?

Davidski said...

You can use PLINK or the much faster PLINK2 in Windows. So you don't need to work in Linux.

K33 said...

Gotcha, thanks David.

I actually finally got shiny tools graph running with the ancestrymap data... wow, this is a really feature-rich suite and I'm just sort of messing around blindly with everything. They also generate FST tables by default (or I think it's "EST", the pairwise stats that supposedly "corrects" the deficiencies of FST)

Hopefully they release a detailed manual on Admixtools2 soon...

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