torstai 21. syyskuuta 2017

Estimates of ancient mixture proportions in present-day Europeans / software

The first Linux script makes possible to generate 23andMe format files from EIGENSTRAT-data and the second one estimates ancient mixture proportions of European people.  Download the full package (without Python interpreter) here.   Instructions are included in the README file.

lauantai 16. syyskuuta 2017

European ancient admixtures

This admixture test was done using the latest data from Reich Laboratory and Dna.Land's Admixture program.  Instead of following the rule and using a mixture triangle Steppe-Farmer-HG I picked also the Central-European Bronze Age to ensure the best coverage of European ancestry.  European Bronze Age was built up from all those three dimensions, so results of all those three roots will be somewhat lower than in tests without the European Bronze Age.  This test works best for Europeans and have obvious blind spots in Africa, Northern America, Near East and Central Asia. I took also some Western Asian samples in the interest of seeing the Iranian and Armenian Neolithic proportions.  

All samples were picked randomly, one sample per population, not as population averages.  No consensus was run.   Both, averaging and consensus calculation would minimize fluctuation in results of minor components, like between Siberian and East-Asian.  The data was converted from the EIGENSTRAT data format I usually use in my tests, of course with exception of the project members.  For that purpose I made a small Bash script which converts Eigenstrat to 23andMe format.  The data and Dna.Land's Admixture program will be soon available here and if anyone see the Eigenstrat-to-23andMe conversion useful I'll include also it to the downloadable library.

sunnuntai 13. elokuuta 2017

Project admixture analyses, revised

Now I used more SNP's with the method coded by Dna.Land authors.  It is now also possible to download all necessary tools for DIY purpose.  It works only on Linux and needs Python to be installed.  Here is a help how to install Python on Ubuntu.

Some comments to understand more about results:

- after a lot of testing I found that the Swedish sample bunch published by the study "No Evidence from Genome-Wide Data of a Khazar Origin for the Ashkenazi Jews" (Behar doesn't fit well with my Swedish project samples and all of them express more Northwest and Central European than the aforementioned Swedish reference.  This happens even if their self-declarations presume some Finnish admixture.   Therefore I decided to label them as East_Scandinavians, which seemed to be correct.  I wonder where they are geographically from.  

- Saami reference samples, unfortunately too few of them were available leading to increased statistic error,  cannot be considered as a source of Siberian.  They represent here a much more diverse source of genetic history.   The small Siberian admixture usually seen in Finnic results is built in Finnish results for the reason that the present-day Siberianness among Finnic people is old and distinct and doesn't match with present Siberians if we simultaneously use also Finnic reference samples.

The summarizing tree:


Finnic 54.6
East_Scandinavian 25.5
Saami 8.0
Northeast_European 5.7
Slavic 2.2
Northwest_European 1.0
Central_European 1.3
AMBIG_European 1.7

Finnic 52.7
Northwest_European 31.3
East_Scandinavian 6.1
Saami 3.8
Northeast_European 2.3
Slavic 1.9
Central_European 1.4

Finnic 72.9
East_Scandinavian 16.3
Saami 3.6
Baltic 3.4
Northwest_European 1.6
Northeast_European 1.7

Finnic 49.1
Northwest_European 25.1
East_Scandinavian 12.9
Northeast_European 5.1
Slavic 2.4
Saami 2.9
Baltic 2.3

Finnic 80.0
East_Scandinavian 13.4
Saami 3.4
Central_European 2.5

Finnic 54.2
East_Scandinavian 27.2
Baltic 9.3
Northwest_European 2.3
Saami 1.8
Northeast_European 1.7
Mediterranean 1.1
Central_European 2.0

Finnic 97.8
AMBIG_European 1.7

Finnic 95.1
East_Scandinavian 2.1
Baltic 1.7
AMBIG_European 1.1

Finnic 85.7
East_Scandinavian 11.9
Baltic 2.1

Finnic 64.0
Saami 31.5
Siberian 2.5
Uralic 1.0

Finnic 92.7
East_Scandinavian 5.2
Saami 2.1

Finnic 83.6
East_Scandinavian 15.2
AMBIG_European 1.1

Finnic 77.7
Baltic 16.8
East_Scandinavian 2.9
AMBIG_European 2.1

Finnic 97.8
AMBIG_European 1.7

Finnic 73.6
East_Scandinavian 14.6
Northwest_European 5.1
Central_European 5.4
Saami 1.0

Finnic 67.8
East_Scandinavian 14.8
Central_European 7.1
Slavic 5.1
Saami 1.4
Mediterranean 1.6
AMBIG_East_European 1.1

Finnic 82.0
East_Scandinavian 12.9
Saami 2.9
Baltic 1.5

Finnic 73.6
East_Scandinavian 14.3
Saami 6.9
Northwest_European 3.8
Slavic 1.0

Finnic 75.8
East_Scandinavian 17.3
Saami 4.6
Slavic 1.8

Finnic 94.0
Saami 2.1
AMBIG_European 2.0
Baltic 1.0

Finnic 94.5
Saami 1.3
Baltic 1.9
AMBIG_European 1.2
AMBIG_East_European 1.1

Finnic 68.8
East_Scandinavian 20.0
Saami 3.6
Northwest_European 3.3
Slavic 2.4
Central_European 1.7

Northwest_European 40.3
East_Scandinavian 22.4
Central_European 15.9
Finnic 9.0
Slavic 4.2
Baltic 3.9
Saami 1.6
Mediterranean 1.7
AMBIG_European 1.0

Northwest_European 52.1
East_Scandinavian 20.5
Finnic 14.8
Slavic 4.1
Central_European 4.3
Baltic 3.9

Northwest_European 59.5
East_Scandinavian 27.3
Central_European 5.4
Baltic 5.8
Saami 1.8

Northwest_European 38.1
East_Scandinavian 32.9
Finnic 11.5
Baltic 9.9
Northeast_European 3.4
Uralic 1.6
Central_European 1.9

Northwest_European 40.8
Finnic 20.7
Northeast_European 13.1
Central_European 9.0
East_Scandinavian 8.4
Slavic 4.0
Saami 2.1
Baltic 1.9

Northwest_European 45.8
East_Scandinavian 31.9
Finnic 11.5
Mediterranean 6.2
Slavic 2.2
Northeast_European 2.1

Although my primary goal was to find out Finnic and Scandinavian admixtures this obviously works fine for almost all Europeans, at least to some extent.

Other samples for a verification purpose:
Irish sample
Northwest_European 90.0
East_Scandinavian 8.7
AMBIG_European 1.3

Western Polish sample
Slavic 49.8
Baltic 18.3
Central_European 14.4
Northwest_European 6.5
Northeast_European 3.5
East_Scandinavian 4.0
Mediterranean 2.3
Uralic 1.1

Sardinian sample
Mediterranean 93.2
Northwest_European 4.5
East_Scandinavian 1.3

Baltic sample
Baltic 70.6
East_Scandinavian 12.3
Slavic 7.9
Northeast_European 6.3
Central_European 2.6
Lithuanian/Yotvingian sample
Baltic 49.0
Slavic 37.5
Central_European 5.8
Mediterranean 4.1
Northeast_European 1.8
AMBIG_European 1.7

Estonian sample
Finnic 41.4
Baltic 19.6
Slavic 16.8
Central_European 9.7
East_Scandinavian 7.8
Saami 2.3
Northeast_European 2.3

Genomes Unzipped sample
Mediterranean 45.7
Northwest_European 19.2
Central_European 19.9
East_Scandinavian 12.3
Slavic 1.9

Genomes Unzipped sample
Mediterranean 37.4
Northwest_European 37.0
East_Scandinavian 15.5
Central_European 9.3

Admixture sums don't give full 100 % because all admixtures below 1% are ignored.

Program downloading and running

Download programs here.  Unzip and locate all programs into a same directory.  To run tests you need use a command line "bash ./ <sample-id>,  where sample-id is the file name holding your genetic data in 23andme format.  The sample file must be compressed with gz file extension (gzip format), but on the command line you give only the sample id (sample-id.gz), not the extension.  The test works fine with following genome builds:  HG18, HG19, GRCh36, GRCh37, but if your genome file is in the FtDna format you have to convert it into the 23andme style.  On Linux it is done easily using four command line entries:

first unzip your genome file and then

cp <original filename> <sample-id>
sed -i 's/\"//g' <sample-id>
sed -i 's/,/\t/g' <sample-id>
gzip <sample-id> 

If your data is already in the 23andme format, but not compressed with gz file extension then you need to unzip it first and run the first and fourth commands explained as above.

edit date 14.8.17 time 17:30

Another Estonian results.  I can only say that it is plausible considering the history

Baltic 37.2
Slavic 29.6
Finnic 22.8
East_Scandinavian 8.1
Saami 1.5

edit 15.8.17 time 17:45

A British results.  It looks like Irish with more Mediterranean and minor Central European admixture..

Northwest_European 81.6
Mediterranean 10.3
Baltic 3.4
Central_European 2.9
AMBIG_European 1.8

tiistai 27. kesäkuuta 2017

Estonian Corded Ware enigma

The following simple dstat-figure shows the mystery of Estonian Corded Ware samples released during this spring.   There can't be any populational continuum from them to present-day Balts, including Estonians.  All thousands years older hunter-gatherer samples are overwhelmingly closer present-day Balts.  The change regarding HG ancestry can be seen in Western and Central Europe where we see a clear cut decrease of HG ancestry, obviously caused by increasing real Corded Ware and Bell Beaker ancestries.   We have to compare pure Neolithic populations against Estonian CW samples to reach parity in the Baltic area.  There is a tiny evidence about the given continuum;  Finns are closer German BA samples than Balts, giving a hint that there could be some subtle continuum.   

lauantai 24. kesäkuuta 2017

Yamnaya and Bell Beaker drift and ratio in present-day Europe

Following statistics gives an insight into how the Bronze Age Steppe ancestry transforms to a modern Northwest European genetic model and gives an idea of differences seen in Europe today.   I made free tests:

f3(Yamnaya Samara, X: Ju_hoan North)
f3(Bell Beaker Germany, X: Ju-hoan_North)
dstat(Bell Beaker Germany, Yamnaya Samara: X, Ju_hoan_North)

All results are based on around 450000 SNP's.

Results of F3_statistics were standardized to a common value 1 and also dstat-results were standardized separately to value 1.  The results show that a Yamnaya type ancestry is still significant in East Europe and the turning line from Yamnaya to Bell Beaker goes from Western Finland to Lithuania and Belarusia.   European farmer or Middle Eastern ancestry becomes dominant in South Europe leading to decreasing Bell Beaker ancestry in absolute terms.

lauantai 17. kesäkuuta 2017

Estonian Corded Ware was not Corded Ware

Despite of the common chronology the Corded Ware in Estonia was genetically a historical misstep if we believe dstat-statistics using samples of German Corded Ware and Bell Beaker cultures.  All Northern Europeans are closer German than Estonian samples.

torstai 15. kesäkuuta 2017

Shared drift with ancient Latvian, Estonian and British samples

Briefly said, shared drift of Latvian samples from Jones et al.   I have rebuild all samples using bam-files straight from the study and a new genotyping algorithm designed for ancient samples.