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Tomenable
23-09-16, 19:49
Post your Eurogenes Steppe K10 results (if you tried this calculator).

I have a very high % of Hindu Kush (6-7 times higher than Polish average from spreadsheet):




Admixture:
Tomenable:
Average of 11 Poles:


WHG-UHG
37.14
39.59


Steppe
29.54
33.87


Near Eastern
29.36
24.41


Hindu Kush
3.32
0.50


Oceanian
0.09
0.18


Siberian
0.05
0.62


East Asian
-
0.16


Amerindian
0.50
0.34


Southeast Asian
-
0.33


Sub-Saharan
-
-




Polish average includes 11 samples: 10H, 11H, 12H, 13H, 14H, 15H, 16H, 6H, 7H, 8H, 9H.

Here is the spreadsheet: https://docs.google.com/spreadsheets/d/1Hb0GVyrf2ztR_QvoIYcmhWtsYv0p39avjqM-G3-6Xew/edit#gid=1809893991


How To:
It’s not complicated. You guys can do it very quickly. Let’s try a last time.

So forget the “readme”. Just follow the steps below.

Let’s presume that LeBrok tested in 23andMe, and that Fluffy tested in FTDNA. LeBrok will download his 23andMe raw data and name the file as LeBrok.txt , while Fluffy will download his FTDNA raw data (Build 37 Raw Data Concatenated) and name the file as Fluffy.csv . Both using Windows.

Download SteppeK10.zip (save icon - an arrow in top right): https://drive.google.com/file/d/0B-X...lRSkcwV0k/view (https://drive.google.com/file/d/0B-XBmvmgdkfVM2RRRHlRSkcwV0k/view)

Extract the files into a folder called SteppeK10, in C:/ . Now you have the folder C:/SteppeK10 , right? Inside it, the files DIYDodecadWin.exe , standardize.r , Steppe.10.F , Steppe.alleles , steppe.par , Steppe.txt .

LeBrok and Fluffy will put the files LeBrok.txt and Fluffy.csv into the folder C:/SteppeK10, respectively.

Download R software: http://cran.utstat.utoronto.ca/bin/w...-3.3.1-win.exe (http://cran.utstat.utoronto.ca/bin/windows/base/R-3.3.1-win.exe)
Install* this program in English and using default options (if you don’t know how to do it, just ask). After that, run it (click in the icon “R x.. 3.3.1” in Desktop).
*I installed just the 64 bits version.

Once R is running, click in “File” (top left), then click in “Change dir”. Select the folder C:/SteppeK10 and click in “ok”.

Do you see the R console? After the “>” character, type the command below and press Enter:
source('standardize.r')

Now:
a. LeBrok, who tested hypothetically with 23andMe, will type the command below, press Enter and wait til he can type anything again:
standardize('LeBrok.txt', company='23andMe')

b. Fluffy will do that with this command:
standardize('Fluffy.csv', company='ftdna')

Finally, you both will type the command below and wait results show up:
system('DIYDodecadWin steppe.par')

Maleth
23-09-16, 20:56
Population

South Asian 0.30
Caucasus 23.11
Southwest Asian13.85
North Amerindian +Arctic -
Siberian-
Mediterranean 29.64
East Asian 0.28
West African 2.25
East European 7.40
North Atlantic 23.17

I am not sure if we are using same calculator but it says Eurogenes k10 (no steppe) but this is using different terms re populations.

Fire Haired14
23-09-16, 22:01
Are you sure this is from Eurogenes? Anyways I can't find it on GEDmatch.

Fluffy
23-09-16, 22:15
Can't find calculator.....

Regio X
23-09-16, 23:08
Download: https://docs.google.com/spreadsheets/d/1Hb0GVyrf2ztR_QvoIYcmhWtsYv0p39avjqM-G3-6Xew/edit?pli=1#gid=1809893991
(source (http://www.anthrogenica.com/showthread.php?4402-eurogenes-steppe-k10&))

See file README.txt.

Regio X
23-09-16, 23:16
Italian (north)

Father's - v4: 17196 SNPs missing (no-call or absent)

44.78% Near_Eastern
0.01% East_Asian
0.00% Siberian
0.49% Oceanian
28.84% WHG-UHG
0.00% Sub-Saharan
7.00% Hindu_Kush
18.85% Steppe
0.03% Amerindian
0.01% Southeast_Asian

Mother's - v4: 17150 SNPs missing

44.34% Near_Eastern
0.00% East_Asian
0.00% Siberian
0.02% Oceanian
30.09% WHG-UHG
0.03% Sub-Saharan
4.15% Hindu_Kush
20.59% Steppe
0.73% Amerindian
0.04% Southeast_Asian

Mine - 23andMe - v4: 17288 SNPs missing


45.57% Near_Eastern
0.00% East_Asian
0.00% Siberian
0.00% Oceanian
28.27% WHG-UHG
0.00% Sub-Saharan
7.02% Hindu_Kush
18.72% Steppe
0.41% Amerindian
0.00% Southeast_Asian

Mine - FTDNA

45.82% Near_Eastern
0.00% East_Asian
0.02% Siberian
0.00% Oceanian
27.91% WHG-UHG
0.00% Sub-Saharan
7.41% Hindu_Kush
18.59% Steppe
0.22% Amerindian
0.03% Southeast_Asian

LeBrok
24-09-16, 05:12
Download: https://docs.google.com/spreadsheets/d/1Hb0GVyrf2ztR_QvoIYcmhWtsYv0p39avjqM-G3-6Xew/edit?pli=1#gid=1809893991
(source (http://www.anthrogenica.com/showthread.php?4402-eurogenes-steppe-k10&))

See file README.txt.
Can't find the readme.txt file. Please, help.

Regio X
24-09-16, 06:36
Can't find the readme.txt file. Please, help.Sorry! Wrong link.

SteppeK10: https://drive.google.com/file/d/0B-XBmvmgdkfVM2RRRHlRSkcwV0k/view

I used R software for Windows. See the "readme": https://drive.google.com/file/d/0B7AJcY18g2GaZGU4OWQ5OWItMzY2NC00NzI1LWIzNWMtMzUxY WI4NjRmMTlk/view

A summary based on the readme file:

1 - Download (https://cran.r-project.org/mirrors.html), install and run R software.

2 - "Once R is running, it will give you a command prompt where you can enter commands. First, you must change the directory to your working directory.
You can do this from the File -> Change dir menu in Windows"

3 - At the R prompt, enter:
source('standardize.r')

"This loads a small program that will convert your data from the
company-specific format to a common format in the next step."

4 - At the R prompt, enter:
a. If you have 23andMe data (either v2 or v3 chip):
standardize('yourgenome.txt', company='23andMe')

b. if you have Family Finder data (Illumina chip only):
standardize('yourgenome.csv', company='ftdna')

5 - At the R prompt, enter:
system('DIYDodecadWin steppe.par')

Maciamo
24-09-16, 11:31
I have a very high % of Hindu Kush (6-7 times higher than Polish average from spreadsheet):

The Hindu Kush corresponds roughly to the Gedrosian admixture in Dodecad and is surely linked to the Steppe PIE too. In this calculator Yamna is 100% Steppe by definition, but eastern Yamna samples didn't yield any R1b-L11, so the Hindu Kush may have come from western Yamna, Kemi-Obla and Maykop. That would make sense since Hindu Kush admixture is quite high in the Caucasus today. Corded Ware samples had between 0% and 8% of Hindu Kush, and German Bell Beaker samples between 0% and 16%.

I ran six Belgian genomes and the Steppe + Hindu Kush was consistently around 26%. Hindu Kush alone was between 3.5% and 7%, but with an average of 5.5% (slightly more than the British samples in the spreadsheet, which range between 1.5% and 6%). So Belgians have considerably more 'Gedrosian' than Poles, which isn't surprising if it was diffused by R1b Proto-Indo-Europeans. After all the Gedrosian admixture is higher in R1b than R1a countries and peaks in Britain and Ireland within Europe.

What in means in your case is that you have more R1b ancestry than the average Poles, which could mean more Celtic, ancient Germanic or medieval/recent German ancestors.

http://cdn.eupedia.com/images/content/Gedrosian-admixture.gif

Tomenable
25-09-16, 01:15
I noticed that Pamiri Tajiks have on average over 40% of Hindu Kush.

They also score a lot of Steppe (Yamnaya) and European Mesolithic (WHG-UHG), as well as Early Neolithic Farmer (Near Eastern).

Amazingly, they only score few % of East Asian, despite living near the border of China:

https://docs.google.com/spreadsheets/d/1Hb0GVyrf2ztR_QvoIYcmhWtsYv0p39avjqM-G3-6Xew/edit#gid=1809893991

http://s17.postimg.org/tnnhdy7hr/Pamir.png

Check the boundaries of the historical region of Pamir:

http://www.heritageinstitute.com/zoroastrianism/tajikistan/page3.htm

http://www.heritageinstitute.com/zoroastrianism/images/maps/PamirBoundaries.jpg

Several photos of Pamiri Tajiks (most of them look very Western Eurasian indeed):

http://www.heritageinstitute.com/zoroastrianism/images/tajikistan/farangees.jpghttp://s17.postimg.org/b7t8d7vfj/Pamiri_man.png

http://s13.postimg.org/55456evuf/Pamiri_girl.pnghttp://s13.postimg.org/ny102m8s7/woman_upper_roshtkala.jpghttp://s14.postimg.org/45p1nk8gx/P1210047_001.jpg

http://s22.postimg.org/cjzxzaqf5/Pamiri_faces_8.jpghttp://www.heritageinstitute.com/zoroastrianism/images/tajikistan/yodgor.jpg

Check also my classification thread, in which some people classified a Pamiri girl as European:

http://www.eupedia.com/forum/threads/32338-Guess-her-ethnicity-and-region

Tomenable
25-09-16, 01:22
"Steppe" component in Eurogenes Steppe K10 is basically the same as "Afanasievo-Yamnaya" component from Gedrosia Eurasia K14 (which is available on GEDmatch), only multiplied by 1,3. For example I score 22,84 "Afanasievo-Yamnaya" in K14, and 29,54 "Steppe" in K10. One Iranian guy scores 9,33 "Afanasievo-Yamnaya" in K14, and 12,48 "Steppe" in K10. So if you don't know how to use Steppe K10, just check how much Yamnaya do you score in Eurasia K14 - and multiply by 1,3 - you will get your "Steppe".

In Eurasia K14 I also score 3,66 percent of "Kalash", which is probably similar to "Hindu Kush" from K10.

How much of "Gedrosia" do Kalash people score? The Kalash are similar to the Baloch people, IIRC.


What in means in your case is that you have more R1b ancestry than the average Poles, which could mean more Celtic, ancient Germanic or medieval/recent German ancestors.

Yes, it is possible.

Alternatively, it could also be from "southerners" (e.g. groups of Armenians who settled in Poland in the Middle Ages and later). I wonder if other Poles from my region also have elevated levels of this, compared to average for the whole country.

Tomenable
25-09-16, 01:54
Sorry, double post. Please delete this one.

Angela
25-09-16, 02:00
I make it a point to live by "If you hear hooves, think horses, not zebras."

Well, unless you're in Africa. Then, in most places, reverse it.

Goga
25-09-16, 02:18
my results:

Near_Eastern ----- 44.35%
Hindu_Kush ----- 35.31%
Steppe ----- 13.35%
WHG-UHG ----- 2.94%
Siberian ----- 1.23%
Amerindian ------ 1.11%
Southeast_Asian ----- 0.92%
East_Asian ----- 0.36%
Sub-Saharan ----- 0.25%
Oceanian ----- 0.17%

8039

Goga
25-09-16, 02:26
Hindu_Kush has to be native Iranid/Aryan (Iranian Plateau neolithic) component. It is high among the Iranian people. Near_Eastern has to be partly Anatolian farmer, partly CHG, partly Levant.


BMAC Aryans who invaded Northern India were full of Hindu_Kush component.


Steppe + WHG-UHG ancestry in me has to be brought by people who brought Y-DNA hg. I2a and E-V13 to Kurdistan from the Steppes/Europe not so long time ago at the time of or after the Medes


I think all other is nothing but noise..

Tomenable
25-09-16, 02:30
my results:

Near_Eastern ----- 44.35%
Hindu_Kush ----- 35.31%
Steppe ----- 13.35%
WHG-UHG ----- 2.94%
Siberian ----- 1.23%
Amerindian ------ 1.11%
Southeast_Asian ----- 0.92%
East_Asian ----- 0.36%
Sub-Saharan ----- 0.25%
Oceanian ----- 0.17%

8039



I will later compare your results to one modern Iranian and one Medieval Iranian ("Iran_recent" from Lazaridis 2016).

"Iran_recent" was a woman who lived around 500-600 years ago (she was dated to 1430–1485 AD) near Ganj Dareh.

==============

Can you post also your Gedrosia Eurasia K14 results (this calculator can be found on Gedmatch)?

Because I'm not sure if "Iran_recent" can be used with Steppe K10. But it can with Eurasia K14.

==============

By the way, "Iran_recent" has been uploaded to Gedmatch - it is kit T637158.

Goga
25-09-16, 02:44
I will later compare your results to one modern Iranian and one Medieval Iranian ("Iran_recent" from Lazaridis 2016).

"Iran_recent" was a woman who lived around 500-600 years ago (she was dated to 1430–1485 AD) near Ganj Dareh.

==============

Can you post also your Gedrosia Eurasia K14 results (this calculator can be found on Gedmatch)?

Because I'm not sure if "Iran_recent" can be used with Steppe K10. But it can with Eurasia K14.
Nice. Take your time.


There are 2 (two) Gedrosia Eurasia K14 calculators on Gedmatch. "Eurasia K14" and "Eurasia K14 Neolithic". Which one do you want?


In general Gedrosia is together with Caucasus my 'highest' components.

Tomenable
25-09-16, 02:46
"Eurasia K14" and "Eurasia K14 Neolithic". Which one do you want?

The "Neolithic" one. I suppose that you will score about 10% of "Afanasievo_Yamnaya" in it.

Goga
25-09-16, 02:55
The "Neolithic" one. I suppose that you will score about 10% of "Afanasievo_Yamnaya" in it.Close.

8040


I don't know why, but so called 'Kalash' and 'S_Indian' are higher. This calculator is nonsense.

+ according to this calculator I'm closest to Hungarian_BA fellas. This calculator is way off...

Goga
25-09-16, 03:20
After all the Gedrosian admixture is higher in R1b than R1a countries.
Maybe in Europe, but on the Iranian Plateau and South Central Asia Gedrosia auDNA correspondents very well with R1a (& J2a). Well, it peaks in so called 'Gedrosia' area and that is in southeast Iran / northwest Pakistan. Birthplace of R1a* ??? , and maybe even R1*...

Goga
25-09-16, 03:31
double post

Goga
25-09-16, 03:36
I noticed that Pamiri Tajiks have on average over 40% of Hindu Kush.

They also score a lot of Steppe (Yamnaya) and European Mesolithic (WHG-UHG), as well as Early Neolithic Farmer (Near Eastern).

Amazingly, they only score few % of East Asian, despite living near the border of China:
Tajiks are Iranian speaking people, they were close to Persians / Farsi folks. But they are heavily mixed with Slavic (Russian) and Turkic tribes. You can compare them to the ancient Steppe Scythians. Like the ancient 'Iraninized' Scythians of the Steppes. Scythians in the Steppes (mixture between Slavic and Turkic tribes) were 'Iranized' by East Iranian people from South East Asia (BMAC / Hindi Kush area).

Capital of Tajikistan is Dushanbe.

Dushanbe is an Iranian/Persian/Kurdish word for 'Monday'.


"Sh (Şem.)" of the word Dushanbe (names of weekdays) has Mesopotamian roots. From

Kurdish names of weekdays


Weekdays
Saturday
Sunday
Monday
Tuesday
Wednesday
Thursday
Friday


Rojî Hefte
Şeme
Yekşeme
Duşeme
Sêşeme
Çarşeme
Pêncşeme
Heyinî


Roja Heftan
Şemî
Yekşem
Duşem
Sêşem
Çarşem
Pêncşem
Înî


Abbreviations
Şe
Ye
Du

Ça

În




The Kurdish name for the first day of the week Sheme (Saturday) is in fact descended from Sumerian Shabbât !!!


Greek - Sabbaton
German - Samstag
Italian - sabato
Spanish - sábado
French - Samedi
Eglish - Saturday
Dutch - zaterdag
Russian - Суббота


https://en.wikipedia.org/wiki/Kurdish_calendar

Tomenable
25-09-16, 04:11
Goga, here is a comparison of your results with another Iranian in Steppe K10:

(BTW, your combined % of Siberian+Amerindian is similar to his East Asian):



Admixture:
Zoran:
Goga:


Near Eastern
44,37
44,35


Hindu Kush
34,81
35,31


Steppe
12,48
13,35


WHG-UHG
5,22
2,94


East Asian
2,17
0,36


Sub Saharan
0,47
0,25


Oceanian
0,42
0,17


Southeast Asian
0,05
0,92


Siberian
-
1,23


Amerindian
-
1,11




This calculator is nonsense.

Yes probably you are right, it might be good for Europeans but not for Iranians.

But I just wanted to check your "Afanasievo_Yamnaya" score in that calculator.

For comparing overall ancestry, I think that HarappaWorld is better for Iranians.

A comparison of your, Iran_recent's and some Iranian results in HarappaWorld:



Admixture:
Zoran:
Arya:
Goga:
Iran 1400s:


Caucasian
40,79
40,88
?
45,47


Baloch
27,95
29,33
?
26,89


SW-Asian
13,29
14,96
?
13,13


NE-Euro
4,30
4,75
?
7,27


Mediterranean
8,05
4,17
?
4,87


S-Indian
2,99
3,71
?
1,23


Siberian
0,96
0,22
?
0,65


W-African
-
-
?
0,20


SE-Asian
-
0,27
?
0,18


Beringian
-
0,26
?
0,12


NE-Asian
-
0,39
?
-


Papuan
0,28
0,92
?
-


American
0,67
-
?
-


San
0,63
-
?
-


E-African
0,07
0,14
?
-


Pygmy
-
-
?
-



Can you post your HarappaWorld results? I will edit this post and add them too.

Goga
25-09-16, 04:39
For comparing overall ancestry, I think that HarappaWorld is better for Iranians.

A comparison of your, Iran_recent's and some Iranian results in HarappaWorld:

...

Can you post your HarappaWorld results? I will edit this post and add them too.
Thanks, but who is this Zoran person? Is (s)he Kurdish? Zoran's auDNA is very similar to me.

My friend, first of all I'm NOT an Iranian-Persian. I'm not from Iran. I'm a 'pure' ethnic Ezdi Kurd born in Georgia (USSR). Because of my native Kurdish religion I'm not mixed with Turks or Arabs/Semites at least for the last 1000 of years. My roots are from both, North and South Kurdistan. Kurds are descendants of the Medes. 2000 years ago Persians and Medes were almost identical to each other and you can see this even nowadays. Even today there are very much similarities between Kurds (Medes) and Iranians (Persians).

But Kurds are DIFFERENT from Persians. Our languages are similar but not the same. It is like differences between Dutch, Danes and Germans..


Ethnically speaking, the closest people to Kurds are Persians, then Caucasians (Georgians, Maykop folks/Adygeans).




Admixture:
Zoran:
Arya:
Goga:
Iran 1400s:


Caucasian
40,79
40,88
40.84
45,47


Baloch
27,95
29,33
27.86
26,89


SW-Asian
13,29
14,96
13.9
13,13


NE-Euro
4,30
4,75
3.92
7,27


Mediterranean
8,05
4,17
8.27
4,87


S-Indian
2,99
3,71
2.23
1,23


Siberian
0,96
0,22
1.08
0,65


W-African
-
-
-
0,20


SE-Asian
-
0,27
0.57
0,18


Beringian
-
0,26
-
0,12


NE-Asian
-
0,39
-
-


Papuan
0,28
0,92
0.36
-


American
0,67
-
0.98
-


San
0,63
-
-
-


E-African
0,07
0,14
-
-


Pygmy
-
-
-
-





8041

Tomenable
25-09-16, 11:45
Thanks, but who is this Zoran person? Is (s)he Kurdish? Zoran's auDNA is very similar to me.

(...)

Kurds are descendants of the Medes.

Zoran is a Western Iranian and he says that his ancestors were Medes and Parthians.

Kurds and Iranians are very similar.


Ethnically speaking, the closest people to Kurds are Persians, then Caucasians (Georgians, Maykop folks/Adygeans).
Also Armenians are close.

Goga
25-09-16, 12:12
Also Armenians are close.Close, but not that close. Armenians are quite different. Armenians are more shifted toward the Levant, Med. Sea. Armenians match better with (and closer to) Druze and Cypriots, than with Kurds, Iranians and Adygeians.

+ Armenian are closer to Georgians than to Iranians, Kurds and Adygeians

Tomenable
25-09-16, 19:55
I compared my results with RISE150 - who lived in what is now Poland, but ~3900 years ago:

I used calculator puntDNAL K15 for this comparison:

1) My result:

Single Population Sharing:

# Population (source) Distance
1 Polish 2.06
2 Swedish 4.03
3 Norwegian 6.35
4 North_German 6.79
5 Belarusian 7.58
6 Slovenian 7.94

2) RISE 150:

Single Population Sharing:

# Population (source) Distance
1 Swedish 5.58
2 North_German 5.95
3 Polish 6.07
4 Slovenian 6.29
5 Norwegian 6.58
6 Hungarian 7.41

She has the same populations as top results in "population sharing" - only in different order.

This cannot be coincidence. RISE150 was a sample of Unetice culture:

http://www.ancestraljourneys.org/copperbronzeagedna.shtml

RISE150 is available on GEDmatch (kit number F999948):

http://www.y-str.org/p/ancient-dna.html

Tomenable
25-09-16, 20:34
Please note, that:

These GEDmatch calculators (such as puntDNAL K15 used above) are good in detecting even very old admixtures, from several thousand years ago. On the other hand, ancestry reports from DNALand, 23andMe or FTDNA are only accurate in showing ancestry no more than up to one thousand years ago. They are good for recent history.

This is why I was very suprised when puntDNAL K15 Oracle showed that I have similar admixture proportions to Swedes, even though according to FTDNA I do not have any Scandinavian admixture.

I understood what is going on only after comparing my results to those of RISE150.

These admixtures have been present here already in the Bronze Age!

====================

My FTDNA report - no any Scandinavian admixture, only Eastern + Central Euro:
(but as I wrote, this report covers accurately only the last 1000 years, at best)

http://s21.postimg.org/65wpcuvgn/FTDNA_my_Origins.png

LeBrok
25-09-16, 21:06
I compared my results with RISE150 - who lived in what is now Poland, but ~3900 years ago:

I used calculator puntDNAL K15 for this comparison:

1) My result:

Single Population Sharing:

# Population (source) Distance
1 Polish 2.06
2 Swedish 4.03
3 Norwegian 6.35
4 North_German 6.79
5 Belarusian 7.58
6 Slovenian 7.94

2) RISE 150:

Single Population Sharing:

# Population (source) Distance
1 Swedish 5.58
2 North_German 5.95
3 Polish 6.07
4 Slovenian 6.29
5 Norwegian 6.58
6 Hungarian 7.41

She has the same populations as top results in "population sharing" - only in different order.

This cannot be coincidence. RISE150 was a sample of Unetice culture:

http://www.ancestraljourneys.org/copperbronzeagedna.shtml

RISE150 is available on GEDmatch (kit number F999948):

http://www.y-str.org/p/ancient-dna.html

They are not too much off, and point to genetic stability since Bronze age in this area. However, do we see a little shift to the East, to Slavic nations?
Do we have any samples from 500BC to 500AD, to see how it looked before Slavic expansion? To have a look at these "Veneti" or Germanic expansion in the area.



1
Polish
1.79


2
Swedish
4.49


3
Belarusian
6.58


4
Norwegian
6.72


5
North_German
7.69


6
Russian
8.03


I'm shifted more East/Slavic than you. Geographically it makes sense too, as my origin is few hundred kilometers more east than yours.

Twilight
25-09-16, 21:10
Sorry! Wrong link.

SteppeK10: https://drive.google.com/file/d/0B-XBmvmgdkfVM2RRRHlRSkcwV0k/view

I used R software for Windows. See the "readme": https://drive.google.com/file/d/0B7AJcY18g2GaZGU4OWQ5OWItMzY2NC00NzI1LWIzNWMtMzUxY WI4NjRmMTlk/view

A summary based on the readme file:

1 - Download (https://cran.r-project.org/mirrors.html), install and run R software.

2 - "Once R is running, it will give you a command prompt where you can enter commands. First, you must change the directory to your working directory.
You can do this from the File -> Change dir menu in Windows"

3 - At the R prompt, enter:
source('standardize.r')

"This loads a small program that will convert your data from the
company-specific format to a common format in the next step."

4 - At the R prompt, enter:
a. If you have 23andMe data (either v2 or v3 chip):
standardize('yourgenome.txt', company='23andMe')

b. if you have Family Finder data (Illumina chip only):
standardize('yourgenome.csv', company='ftdna')

5 - At the R prompt, enter:
system('DIYDodecadWin steppe.par')

Im afraid my IPad can't download using the R software. Do you knowing there is a way for my IPad to download Steepes10?

LeBrok
25-09-16, 21:20
Im afraid my IPad can't download using the R software. Do you knowing there is a way for my IPad to download Steepes10?
It is not going well for me either, I've downloaded all but can't quickly figure out all the necessary steps. Foreign concept for me to run programs in a program and have with weird names to the right folders. I don't want to spend hours with this to experiment endlessly what works. I need baby steps manual, if someone cares to right them down.

LeBrok
25-09-16, 21:28
I compared my results with RISE150 - who lived in what is now Poland, but ~3900 years ago:



2) RISE 150:

Single Population Sharing:

# Population (source) Distance
1 Swedish 5.58
2 North_German 5.95
3 Polish 6.07
4 Slovenian 6.29
5 Norwegian 6.58
6 Hungarian 7.41


What is very interesting is the fact that Rise 150 is almost at equal distance to modern populations of Germanics and Slavs of the Area. All from 5.58 to 6.58, that's a very small margin to fit all in. This must be true Corded Ware heritage for both groups.

Tomenable
25-09-16, 21:31
Now I tried 1-to-1 comparison:

Comparing Kit T269964 (*Tomenable) and F999948 (RISE150,Poland,3.4ky):

Minimum threshold size to be included in total = 25 SNPs
Mismatch-bunching Limit = 25 SNPs
Minimum segment cM to be included in total = 1.0 cM

Largest segment = 4.7 cM
Total of segments > 1 cM = 1,142.2 cM
701 matching segments

307164 SNPs used for this comparison.

Comparison took 0.03335 seconds.

===================================

Comparing Kit T269964 (*Tomenable) and F999933 (BR2, Hungary, 3.2ky):

Minimum threshold size to be included in total = 25 SNPs
Mismatch-bunching Limit = 25 SNPs
Minimum segment cM to be included in total = 1.0 cM

Largest segment = 6.8 cM
Total of segments > 1 cM = 1,488.4 cM
921 matching segments

657082 SNPs used for this comparison.

Comparison took 0.04641 seconds.

=============
=============

I have 701 matching segments with RISE150 and a bit more (921) with Hungarian BR2.

However, Hungarian BR2 is not similar to me and to RISE150 in "Single Population Sharing".

In puntDNAL K15:

3) BR2 (Kyjatice culture):

Single Population Sharing:

# Population (source) Distance
1 Utahn_White 4.41
2 South_German 4.52
3 French 5.02
4 English 6
5 Orcadian 6.91
6 Scottish 7.3
7 Irish 7.61

BR2 has totally different populations (no Poles, no Swedes, no Slovenians, no Norwegians, etc.).

I'm not sure how to interpret this (why more of matching segments, if less matching populations?).

LeBrok
25-09-16, 21:55
Now I tried 1-to-1 comparison:

Comparing Kit T269964 (*Tomenable) and F999948 (RISE150,Poland,3.4ky):

Minimum threshold size to be included in total = 25 SNPs
Mismatch-bunching Limit = 25 SNPs
Minimum segment cM to be included in total = 1.0 cM

Largest segment = 4.7 cM
Total of segments > 1 cM = 1,142.2 cM
701 matching segments

307164 SNPs used for this comparison.

Comparison took 0.03335 seconds.

===================================

Comparing Kit T269964 (*Tomenable) and F999933 (BR2, Hungary, 3.2ky):

Minimum threshold size to be included in total = 25 SNPs
Mismatch-bunching Limit = 25 SNPs
Minimum segment cM to be included in total = 1.0 cM

Largest segment = 6.8 cM
Total of segments > 1 cM = 1,488.4 cM
921 matching segments

657082 SNPs used for this comparison.

Comparison took 0.04641 seconds.

=============
=============

I have 701 matching segments with RISE150 and a bit more (921) with Hungarian BR2.

However, Hungarian BR2 is not similar to me and to RISE150 in "Single Population Sharing".

In puntDNAL K15:

3) BR2 (Kyjatice culture):

Single Population Sharing:

# Population (source) Distance
1 Utahn_White 4.41
2 South_German 4.52
3 French 5.02
4 English 6
5 Orcadian 6.91
6 Scottish 7.3
7 Irish 7.61

BR2 has totally different populations (no Poles, no Swedes, no Slovenians, no Norwegians, etc.).

I'm not sure how to interpret this (why more of matching segments, if less matching populations?). Because the other populations are even closer to him than you. For example French can have: Total of segments > 1 cM = 1,600 cM and 1002 matching segments

I wonder if BR2 is the source of Celtic type IEs?

Tomenable
25-09-16, 22:11
I carried out also a 1-to-1 comparison with Hinxton-4 (Iron Age Briton) - just to make sure that I'm not as closely related to Ancient Britons as to RISE150 (which would imply that there is nothing special about this similarity with RISE150):

Comparing Kit T269964 (*Tomenable) and F999925 (Hinxton-4, UK, 2ky):

Minimum threshold size to be included in total = 25 SNPs
Mismatch-bunching Limit = 25 SNPs
Minimum segment cM to be included in total = 1.0 cM

Largest segment = 2.7 cM
Total of segments > 1 cM = 162.9 cM
125 matching segments

575225 SNPs used for this comparison.

Comparison took 0.02972 seconds.

========================

Only 125 segments, much fewer than with RISE150 and BR2.

LeBrok
25-09-16, 22:30
I carried out also a 1-to-1 comparison with Hinxton-4 (Iron Age Briton) - just to make sure that I'm not as closely related to Ancient Britons as to RISE150 (which would imply that there is nothing special about this similarity with RISE150):

Comparing Kit T269964 (*Tomenable) and F999925 (Hinxton-4, UK, 2ky):

Minimum threshold size to be included in total = 25 SNPs
Mismatch-bunching Limit = 25 SNPs
Minimum segment cM to be included in total = 1.0 cM

Largest segment = 2.7 cM
Total of segments > 1 cM = 162.9 cM
125 matching segments

575225 SNPs used for this comparison.

Comparison took 0.02972 seconds.

========================

Only 125 segments, much fewer than with RISE150 and BR2.
That's a bit weird perhaps, but keep in mind that matches will be fewer if we are not dealing with the whole genome. Many ancient genomes are only partial.

Fluffy
25-09-16, 22:42
It is not going well for me either, I've downloaded all but can't quickly figure out all the necessary steps. Foreign concept for me to run programs in a program and have with weird names to the right folders. I don't want to spend hours with this to experiment endlessly what works. I need baby steps manual, if someone cares to right them down.

LOL same here man. I can't figure this out unless I am willing to spend hours to study it.

Tomenable
25-09-16, 23:17
Some more ancients in puntDNAL K15 calculator:

Iron Age Celtic Briton was most similar to modern Irish, Anglo-Saxon to modern Swedes:

Hinxton-4 (Celtic Briton, 2000 ybp):

Kit F999925. Single Population Sharing:

# Population (source) Distance
1 Irish 2.38
2 North_German 2.95
3 Orcadian 3.03
4 English 3.05
5 Scottish 3.18
6 Norwegian 4.4
7 Slovenian 4.44
8 Austrian 4.91

Hinxton-2 (Anglo-Saxon, 1300 ybp):

Kit F999921. Single Population Sharing:

# Population (source) Distance
1 Swedish 4.3
2 Norwegian 4.41
3 Scottish 5.73
4 North_German 5.87
5 Polish 6.44
6 Orcadian 6.82
7 English 7.24
8 Irish 7.93

==========================

It is quite surprising, that North Germans are similar both to Celtic Briton & to Anglo-Saxon.

Even more surprising, that Germans are more similar to Celtic Briton than to Saxon.

Perhaps she (Hinxton-2) was not even a Saxon, but either an Angle or a Jute.

==========================

Modern English are closer to Celtic Briton (distance 3.05) than to unmixed Anglo-Jute-Saxon (distance 7.24). This is in agreement with recent studies (from 2015-2016) which showed that the English have mostly Celtic / Briton ancestry.

"Pure Anglo-Saxon-Jutes" were Scandinavian-like rather than English-like or German-like.

This also shows why it is hard to distinguish Anglo-Saxon-Jute and Danish-Swedish Viking ancestry.

Only Norwegian Viking ancestry can be distinguished, because Norwegians are a bit different.

Twilight
26-09-16, 00:05
It is not going well for me either, I've downloaded all but can't quickly figure out all the necessary steps. Foreign concept for me to run programs in a program and have with weird names to the right folders. I don't want to spend hours with this to experiment endlessly what works. I need baby steps manual, if someone cares to right them down.

LOL same here man. I can't figure this out unless I am willing to spend hours to study it.

Im glad I'm not the only one, hopefully our personal results will come to us soon. :)
Best of luck to Davidski, it appears that near Eastern genome among Bedouins in 60% and 2% WHG so SteepesK10 sounds promising. :)

LeBrok
26-09-16, 00:16
I share 701 matching segments with RISE150 and 921 with BR2.

Numbers such as 701 - 921 matching segments seem to be a lot.

I made a similar comparison with ancient and modern Iranians:

Kit T637158 (Medieval Iranian) shares 758 segments with a modern Iranian.

Kit M124870 (Copper Age Iranian) shares 597 segments with a modern Iranian.

Finally, T637158 and M124870 share 380 matching segments with each other.

Criteria of comparison were the same in each case:
As I said before, perhaps it depends how much ancient DNA was recovered? Most of them are partial.

Goga
26-09-16, 01:39
He already had almost 11% SW Asian, and modern people have only 13-15%.

It's the North East European and Mediterranean that he's missing. The North East European could have come with steppe people in the Bronze or even the Iron Age, and so could the little bit of Mediterranean as well perhaps. The Srubnaya, Andronovo type people were, what, 40% Middle Neolithic as well as EHG?
It was introduced after some Medes migrated into Balochistan. The Balochi language is a branch of Northwestern Iranian languages (like Kurdish) and it has been said it is from Kurdistan than arrived with the Medes.
Those Medes who migrated into Balochistan missed that 'North East European' and 'Mediterranean' components. So those components entered Kurdistan and West Iran not so long time ago. And Baloch people miss Y-DNA hg. I2a and E-V13.

Y-DNA hg. I2a and E-V13 (European type) is in Kurdistan and Western Iran from recent times and I'm sure that those who brought Y-DNA hg. I2a and E-V13 to Kurdistan were those who also brought 'North East European' and 'Mediterranean' components.


'Purest' Iranians (Aryans) were Caucaso-Gedrosia folks with some minor SW Asian influences.


The Aryan Medes had nothing to do with the the 'North East European' and 'Mediterranean' components. Baloch folks don't have these components, but their Gedrosia component is higher than that of Kurds & Persians.


'North East European' and 'Mediterranean' components are VERY recent in Kurdistan and have something to do with these:


Back migration of the Iranic speaking Scythians from Ukraine????


http://cdn.eupedia.com/images/content/Haplogroup_I2a.gif
http://cdn.eupedia.com/images/content/Haplogroup-E-V13.gif

Goga
26-09-16, 01:48
It seems that there was a some kind of a migration from the Balkans into the western parts of the Iranian Plateau, and Aryans (West Iranian like the Medes and Persians) mixed a little bit with those people. Maybe from the Indo-European West Anatolians like the Hittites and Phrygia or something???


Y-DNA hg. I2a and E-V13 are not native to Iranian/Aryans otherwise there would be some Y-DNA hg. I2a and E-V13 in BMAC and SouthCentral Asia or even in India.

Regio X
26-09-16, 02:24
Im afraid my IPad can't download using the R software. Do you knowing there is a way for my IPad to download Steepes10?I don’t know about iPad, because I don’t use it. I wonder if it could easily run an “exe” anyway. I’m afraid not. I hope someone else can help you in this regard.

Btw, there is a R version for Mac, but "readme" states that this process specifically demand a Windows or Linux machine. Particularly, I used Windows.


It is not going well for me either, I've downloaded all but can't quickly figure out all the necessary steps. Foreign concept for me to run programs in a program and have with weird names to the right folders. I don't want to spend hours with this to experiment endlessly what works. I need baby steps manual, if someone cares to right them down.

LOL same here man. I can't figure this out unless I am willing to spend hours to study it.It’s not complicated. You guys can do it very quickly. Let’s try a last time.

So forget the “readme”. Just follow the steps below.

Let’s presume that LeBrok tested in 23andMe, and that Fluffy tested in FTDNA. LeBrok will download his 23andMe raw data and name the file as LeBrok.txt , while Fluffy will download his FTDNA raw data (Build 37 Raw Data Concatenated) and name the file as Fluffy.csv . Both using Windows.

Download SteppeK10.zip (save icon - an arrow in top right): https://drive.google.com/file/d/0B-X...lRSkcwV0k/view (https://drive.google.com/file/d/0B-XBmvmgdkfVM2RRRHlRSkcwV0k/view)

Extract the files into a folder called SteppeK10, in C:/ . Now you have the folder C:/SteppeK10 , right? Inside it, the files DIYDodecadWin.exe , standardize.r , Steppe.10.F , Steppe.alleles , steppe.par , Steppe.txt .

LeBrok and Fluffy will put the files LeBrok.txt and Fluffy.csv into the folder C:/SteppeK10, respectively.

Download R software: http://cran.utstat.utoronto.ca/bin/windows/base/R-3.3.1-win.exe
Install* this program in English and using default options (if you don’t know how to do it, just ask). After that, run it (click in the icon “R x.. 3.3.1” in Desktop).
*I installed just the 64 bits version.

Once R is running, click in “File” (top left), then click in “Change dir”. Select the folder C:/SteppeK10 and click in “ok”.

Do you see the R console? After the “>” character, type the command below and press Enter:
source('standardize.r')

Now:
a. LeBrok, who tested hypothetically with 23andMe, will type the command below, press Enter and wait til he can type anything again:
standardize('LeBrok.txt', company='23andMe')

b. Fluffy will do that with this command:
standardize('Fluffy.csv', company='ftdna')

Finally, you both will type the command below and wait results show up:
system('DIYDodecadWin steppe.par')

Goga
26-09-16, 02:44
Now:
a. LeBrok, who tested hypothetically with 23andMe, will type the command below, click in Enter and wait til he can type anything again:
standardize('LeBrok.txt', company='23andMe')

b. Fluffy will do that with this command:
standardize('Fluffy.csv', company='ftdna')

Finally, you both will type the command below and wait results show up:
system('DIYDodecadWin steppe.par')
correction

"standardize('LeBrok.txt', company='23andMe')" must be
"standardize ('LeBrok.txt', company='23andMe') ----> space bar between "standardize" and "('LeBrok.txt', company='23andMe')"

"standardize('Fluffy.csv', company='ftdna')" must be
"standardize ('Fluffy.csv', company='ftdna')" ----> space bar between "standardize" and ('Fluffy.csv', company='ftdna')


"system('DIYDodecadWin steppe.par')" must be
"system ('DIYDodecadWin steppe.par')" ----> space bar between "system" and "('DIYDodecadWin steppe.par')"

Regio X
26-09-16, 03:32
correction

"standardize('LeBrok.txt', company='23andMe')" must be
"standardize ('LeBrok.txt', company='23andMe') ----> space bar between "standardize" and "('LeBrok.txt', company='23andMe')"

"standardize('Fluffy.csv', company='ftdna')" must be
"standardize ('Fluffy.csv', company='ftdna')" ----> space bar between "standardize" and ('Fluffy.csv', company='ftdna')


"system('DIYDodecadWin steppe.par')" must be
"system ('DIYDodecadWin steppe.par')" ----> space bar between "system" and "('DIYDodecadWin steppe.par')" Well, here it works without the spaces. I haven't tried with them.

LeBrok
26-09-16, 04:39
I don’t know about iPad, because I don’t use it. I wonder if it could easily run an “exe” anyway. I’m afraid not. I hope someone else can help you in this regard.

Btw, there is a R version for Mac, but "readme" states that this process specifically demand a Windows or Linux machine. Particularly, I used Windows.


It’s not complicated. You guys can do it very quickly. Let’s try a last time.

So forget the “readme”. Just follow the steps below.

Let’s presume that LeBrok tested in 23andMe, and that Fluffy tested in FTDNA. LeBrok will download his 23andMe raw data and name the file as LeBrok.txt , while Fluffy will download his FTDNA raw data (Build 37 Raw Data Concatenated) and name the file as Fluffy.csv . Both using Windows.

Download SteppeK10.zip (save icon - an arrow in top right): https://drive.google.com/file/d/0B-X...lRSkcwV0k/view (https://drive.google.com/file/d/0B-XBmvmgdkfVM2RRRHlRSkcwV0k/view)

Extract the files into a folder called SteppeK10, in C:/ . Now you have the folder C:/SteppeK10 , right? Inside it, the files DIYDodecadWin.exe , standardize.r , Steppe.10.F , Steppe.alleles , steppe.par , Steppe.txt .

LeBrok and Fluffy will put the files LeBrok.txt and Fluffy.csv into the folder C:/SteppeK10, respectively.

Download R software: http://cran.utstat.utoronto.ca/bin/windows/base/R-3.3.1-win.exe
Install* this program in English and using default options (if you don’t know how to do it, just ask). After that, run it (click in the icon “R x.. 3.3.1” in Desktop).
*I installed just the 64 bits version.

Once R is running, click in “File” (top left), then click in “Change dir”. Select the folder C:/SteppeK10 and click in “ok”.

Do you see the R console? After the “>” character, type the command below and press Enter:
source('standardize.r')

Now:
a. LeBrok, who tested hypothetically with 23andMe, will type the command below, press Enter and wait til he can type anything again:
standardize('LeBrok.txt', company='23andMe')

b. Fluffy will do that with this command:
standardize('Fluffy.csv', company='ftdna')

Finally, you both will type the command below and wait results show up:
system('DIYDodecadWin steppe.par')
Thanks for babysteps :), it worked like a charm.

I took some liberty and updated first post adding this as tutorial.

LeBrok
26-09-16, 04:56
Admixture:
Tomenable:
Average of 11 Poles:
LeBrok:
LeBrok's
Wife


WHG-UHG
37.14
39.59
38.73
37.53


Steppe
29.54
33.87
29.01
30.09


Near Eastern
29.36
24.41
26.77
28.12


Hindu Kush
3.32
0.50
3.50
2.25


Oceanian
0.09
0.18
0.00
0.00


Siberian
0.05
0.62
0.33
1.2


East Asian
-
0.16
1.09
0.35


Amerindian
0.50
0.34
0.09
0.12


Southeast Asian
-
0.33
0.48
0.33



The "average" group of Poles was really high on WHG and Steppe and low on Farmer. I wonder what region they were from?
Surprisingly, for a guy who loves HGs, your Farmer/Near Eastern is the highest, Tomenable. ;)

I might have 1 percent of Tatar, East Asian, lol.

How did Hindu Kush got to Poland? With Gypsies? It is too elevated to be explained with few Gypsies in Poland, must be something else. The unknown history of Poland...

Tomenable
26-09-16, 06:57
Regio & Goga thanks for helping other users, and LeBrok thanks for adding the tutorial.

I should have done that myself because it is my thread after all, sorry!

Tomenable
26-09-16, 08:22
Here is a list of some (but not all) of ancient samples which are on Gedmatch:

(for example Celtic Briton Hinxton-4 is kit F999925 on Gedmatch):

http://www.y-str.org/p/ancient-dna.html

This list was last updated in 2014 or early 2015, so it doesn't have recent ones.

The author no longer updates it because he now became an orthodox Christian:

http://www.y-str.org/2016/07/focusing-on-trumpet-call-from-now-on.html
(http://www.y-str.org/2016/07/focusing-on-trumpet-call-from-now-on.html)

I had ceased developing Genetic Genealogy Tools last year. (...) I am called for a greater cause, to warn people and preach the true gospel message of repentance which leads to salvation. I started Trumpet Call, to be a watchman and warn people of the coming God's wrath which is lacking in today's churches.

You can be a Christian fanatic and still update your ancient DNA database, LOL.

Why did he stop?! :(

Volat
26-09-16, 18:54
----------------------------
FINAL ADMIXTURE PROPORTIONS:
----------------------------

20.23% Near_Eastern
0.24% East_Asian
0.07% Siberian
0.00% Oceanian
41.10% WHG-UHG
0.00% Sub-Saharan
0.88% Hindu_Kush
37.38% Steppe
0.09% Amerindian
0.01% Southeast_Asian

Volat
27-09-16, 19:58
If can compile results of K10 steppes on this forum in a spreadsheet, then I can put the results on PCA plot. Out of curiosity how we are spread out.

Tomenable
27-09-16, 20:00
If can compile results of K10 steppes on this forum in a spreadsheet, then I can put the results on PCA plot. Out of curiosity how we are spread out.

Great idea, thanks!

Tomenable
27-09-16, 20:30
----------------------------
FINAL ADMIXTURE PROPORTIONS:
----------------------------

20.23% Near_Eastern
0.24% East_Asian
0.07% Siberian
0.00% Oceanian
41.10% WHG-UHG
0.00% Sub-Saharan
0.88% Hindu_Kush
37.38% Steppe
0.09% Amerindian
0.01% Southeast_Asian

Here is a guy from Saint Petersburg for comparison:

20.25% Near_Eastern
0.72% East_Asian
2.92% Siberian
0.27% Oceanian
38.14% WHG-UHG
0.10% Sub-Saharan
2.53% Hindu_Kush
34.59% Steppe
0.48% Amerindian
0.00% Southeast_Asian

Volat
27-09-16, 20:40
Here is a guy from Saint Petersburg for comparison:

20.25% Near_Eastern
0.72% East_Asian
2.92% Siberian
0.27% Oceanian
38.14% WHG-UHG
0.10% Sub-Saharan
2.53% Hindu_Kush
34.59% Steppe
0.48% Amerindian
0.00% Southeast_Asian

St-Petersburg is ethnically so diverse, with people settled it from all over Russia, Ukraine and other republics.

Volat
27-09-16, 20:51
St-Petersburg is ethnically so diverse, with people settled it from all over Russia, Ukraine and other republics.

A city such as Novosibirsk, considered to be capital of Siberia is more Russian and Slavic than St-Petersburg.

Goga
27-09-16, 21:00
Here is a guy from Saint Petersburg for comparison:

20.25% Near_Eastern
0.72% East_Asian
2.92% Siberian
0.27% Oceanian
38.14% WHG-UHG
0.10% Sub-Saharan
2.53% Hindu_Kush
34.59% Steppe
0.48% Amerindian
0.00% Southeast_AsianThanks. This is very interesting. I expected more of the East_Asian + Siberian components. This is a surprise!

Goga
27-09-16, 21:03
A city such as Novosibirsk, considered to be capital of Siberia is more Russian and Slavic than St-Petersburg.Why, what do you mean by that?


Also maybe that Russian fella from St-Petersburg is not really native to that city. So you need much more samples and examples to determine an average of that city

Volat
27-09-16, 21:17
Thanks. This is very interesting. I expected more of the East_Asian + Siberian components. This is a surprise!

Expected more? Take a look at large samples of Russians in the spreadsheet Tomenable posted. Russians have little east asian and siberian components.

Volat
27-09-16, 21:19
Why, what do you mean by that?


Also maybe that Russian fella from St-Petersburg is not really native to that city. So you need much more samples and examples to determine an average of that city

What are you not clear of? St-Petersburg is a large city of around 5mln populated by peoples of all kind of ethnicities from all over former Russian empire and USSR. They don't represent people of north-western Russia. People of regional areas surrounding St-Petersburg represent north-western Russians.

Goga
27-09-16, 21:36
Expected more? Take a look at large samples of Russians in the spreadsheet Tomenable posted. Russians have little east asian and siberian components.Maybe I made a mistake. St-Petersburg is a northern city, close to Finland and other Finno-Ugric people. There is lots of Y-DNA hg. N1c1 in that are.

Hg. N1c1 has to be part of WHG-UHG. I made a mistake because I didn't think about that.

Goga
27-09-16, 21:39
What are you not clear of? St-Petersburg is a large city of around 5mln populated by peoples of all kind of ethnicities from all over former Russian empire and USSR. They don't represent people of north-western Russia. People of regional areas surrounding St-Petersburg represent north-western Russians.Yeah, I do agree with you. Everywhere in the world cities/centers are always more mixed than in hinterland/periphery.

Volat
27-09-16, 21:43
Maybe I made a mistake. St-Petersburg is a northern city, close to Finland and other Finno-Ugric people. There is lots of Y-DNA hg. N1c1 in that are.

Hg. N1c1 has to be part of WHG-UHG. I made a mistake because I didn't think about that.

Yes, you made a mistake because population of St-Petersburg is not typical of that found in north-western Russia around Finland.

Tomenable
27-09-16, 22:23
What I said is that Kurds are DIRECT descendants of the Medes. The Medes lived in the Iron Age in Media/Persian/Iran. Kurds and Kurdish language are NATIVE to their homeland.

Yes, genetic data confirms that there is continuity from the Iron Age (since year 1000 BCE).

We have a Copper Age Iranian, and an Iron Age Iranian. But we still lack a Bronze Age one.


St-Petersburg is ethnically so diverse, with people settled it from all over Russia, Ukraine and other republics.

Yeah, big cities are melting pots with people from various regions. We need rural samples.

Hauteville
28-09-16, 11:03
Why not available on GEDmatch?

Tomenable
15-10-16, 21:16
LeBrok,

Your wife also scores quite a lot of Hindu Kush - is she from Cracow?

You are 1/4 from Cracow and 3/4 from South-Eastern Mazovia, right?

Twilight
22-10-16, 22:00
I don’t know about iPad, because I don’t use it. I wonder if it could easily run an “exe” anyway. I’m afraid not. I hope someone else can help you in this regard.

Btw, there is a R version for Mac, but "readme" states that this process specifically demand a Windows or Linux machine. Particularly, I used Windows.


It’s not complicated. You guys can do it very quickly. Let’s try a last time.

So forget the “readme”. Just follow the steps below.

Let’s presume that LeBrok tested in 23andMe, and that Fluffy tested in FTDNA. LeBrok will download his 23andMe raw data and name the file as LeBrok.txt , while Fluffy will download his FTDNA raw data (Build 37 Raw Data Concatenated) and name the file as Fluffy.csv . Both using Windows.

Download SteppeK10.zip (save icon - an arrow in top right): https://drive.google.com/file/d/0B-X...lRSkcwV0k/view (https://drive.google.com/file/d/0B-XBmvmgdkfVM2RRRHlRSkcwV0k/view)

Extract the files into a folder called SteppeK10, in C:/ . Now you have the folder C:/SteppeK10 , right? Inside it, the files DIYDodecadWin.exe , standardize.r , Steppe.10.F , Steppe.alleles , steppe.par , Steppe.txt .

LeBrok and Fluffy will put the files LeBrok.txt and Fluffy.csv into the folder C:/SteppeK10, respectively.

Download R software: http://cran.utstat.utoronto.ca/bin/windows/base/R-3.3.1-win.exe
Install* this program in English and using default options (if you don’t know how to do it, just ask). After that, run it (click in the icon “R x.. 3.3.1” in Desktop).
*I installed just the 64 bits version.

Once R is running, click in “File” (top left), then click in “Change dir”. Select the folder C:/SteppeK10 and click in “ok”.

Do you see the R console? After the “>” character, type the command below and press Enter:
source('standardize.r')

Now:
a. LeBrok, who tested hypothetically with 23andMe, will type the command below, press Enter and wait til he can type anything again:
standardize('LeBrok.txt', company='23andMe')

b. Fluffy will do that with this command:
standardize('Fluffy.csv', company='ftdna')

Finally, you both will type the command below and wait results show up:
system('DIYDodecadWin steppe.par')

Bold= Stuck on tis part

Okay, looks like I got into a check point and Downloaded the R console. But next to ">" when I typed ('Simon_Van_Giesen.txt', company='23andMe') , I got an error. Is there something I'm missing?

Regio X
22-10-16, 22:07
Bold= Stuck on tis part

Okay, looks like I got into a check point and Downloaded the R console. But next to ">" when I typed ('Simon_Van_Giesen.txt', company='23andMe') , I got an error. Is there something I'm missing?What is the error message?

Twilight
22-10-16, 22:30
What is the error message?

Here you go:)

> ('Simon_Van_Giesen.txt', company='23andMe')
Error: unexpected ',' in "('Simon_Van_Giesen.txt',"
>

Regio X
23-10-16, 00:05
Deleted by poster

Regio X
23-10-16, 00:33
Here you go:)

> ('Simon_Van_Giesen.txt', company='23andMe')
Error: unexpected ',' in "('Simon_Van_Giesen.txt',"
>Oh! And it seems that you forgot the command "standardize".
It would be as follow:
standardize ('Simon_Van_Giesen.txt', company='23andMe')

Twilight
23-10-16, 04:39
Oh! And it seems that you forgot the command "standardize".
It would be as follow:
standardize ('Simon_Van_Giesen.txt', company='23andMe')

I guess it goes to show how good a computer technician I am :D. I suppose I can look at the directions tomorrow when my mind is fresh. Thanks for the tip Regio :)

davef
23-10-16, 05:44
I guess it goes to show how good a computer technician I am :D. I suppose I can look at the directions tomorrow when my mind is fresh. Thanks for the tip Regio :)

Yeah, I tend to question how good of a programmer I am at times when I try to code or think at 8 pm when the adderall and caffeine is worn out and I'm in stupid mode. lol
Adderall+complex carbs(I eat oatmeal and raisins for lunch every day)+aerobic exercise+caffeine+not being sleep deprived+b-12=smartiness,at least in my case....

Templar
24-10-16, 06:22
Hindu_Kush has to be native Iranid/Aryan (Iranian Plateau neolithic) component. It is high among the Iranian people. Near_Eastern has to be partly Anatolian farmer, partly CHG, partly Levant.


BMAC Aryans who invaded Northern India were full of Hindu_Kush component.


Steppe + WHG-UHG ancestry in me has to be brought by people who brought Y-DNA hg. I2a and E-V13 to Kurdistan from the Steppes/Europe not so long time ago at the time of or after the Medes


I think all other is nothing but noise..

Iranic people didn't live in the Middle East during the neolithic. They came around 1500-1000 BC.


https://en.wikipedia.org/wiki/Iranian_peoples

Dibran
07-05-17, 19:44
Does this not work with v4 23 results? I keep following it to a T and get an error when entering my file name in the command prompt.

Dibran
07-05-17, 19:48
Oh! And it seems that you forgot the command "standardize".
It would be as follow:
standardize ('Simon_Van_Giesen.txt', company='23andMe')

I am stuck on part b. my file is v4( which is not indicated in your instructions as workable)

This is my error as follows:

standardize('Hamit.txt', company='23andMe')

Error in file(file, "rt") : cannot open the connection
In addition: Warning message:
In file(file, "rt") :
cannot open file 'hamit.txt': No such file or directory

Promenade
08-05-17, 00:34
Can anyone assist me with the final part?

I type in - system('DIYDodecadWin steppe.par') and I get an error message saying "/bin/sh: DIYDodecadWin: command not found"

The file DIYDodecadWin.exe is certainly in the folder though.

I'm using a Mac, not sure if that makes a difference. I was able to get through everything else so far.

Aha
10-05-17, 00:28
Can anyone assist me with the final part?

I type in - system('DIYDodecadWin steppe.par') and I get an error message saying "/bin/sh: DIYDodecadWin: command not found"

The file DIYDodecadWin.exe is certainly in the folder though.

I'm using a Mac, not sure if that makes a difference. I was able to get through everything else so far.

If I am not mistaken, dodecad comes for win and linux both. The "win" means the file is for windows. And you will probably need to emulate windows or linux on your mac in order for it to work

Aha
10-05-17, 00:32
My data
Ukrainian, Kyiv

FINAL ADMIXTURE PROPORTIONS:
----------------------------



WHG-UHG
35.80%


Steppe
30.53%


Near_Eastern
26.03%


Hindu_Kush
5.33%


Siberian
2.13%


Southeast_Asian
0.11%


Oceanian
0.03%


East_Asian
0.02%


Amerindian
0.01%


Sub-Saharan
0.00%

Regio X
10-05-17, 01:57
I am stuck on part b. my file is v4( which is not indicated in your instructions as workable)

This is my error as follows:

standardize('Hamit.txt', company='23andMe')

Error in file(file, "rt") : cannot open the connection
In addition: Warning message:
In file(file, "rt") :
cannot open file 'hamit.txt': No such file or directoryYes, it works with v4.
This message of error showed up because the Hamit.txt was not found. You have to put it into the folder 'SteppeK10' (in the example), i.e., together the files you downloaded. See below.


Download SteppeK10.zip (save icon - an arrow in top right): https://drive.google.com/file/d/0B-X...lRSkcwV0k/view (https://drive.google.com/file/d/0B-XBmvmgdkfVM2RRRHlRSkcwV0k/view)

Extract the files into a folder called SteppeK10, in C:/ . Now you have the folder C:/SteppeK10 , right? Put the file Hamit.txt into the folder C:/SteppeK10. Inside it, there are now the files DIYDodecadWin.exe , standardize.r , Steppe.10.F , Steppe.alleles , steppe.par , Steppe.txt and Hamit.txt.

Download R software: http://cran.utstat.utoronto.ca/bin/windows/base/R-3.3.1-win.exe
Install

Once R is running, click in “File” (top left), then click in “Change dir”. Select the folder C:/SteppeK10 and click in “ok”.

Do you see the R console? After the “>” character, type the command below and press Enter:
source('standardize.r')

Type the command below, press Enter and wait till you can type anything again:
standardize('Hamit.txt', company='23andMe')

Finally, you will type the command below and wait results show up:
system('DIYDodecadWin steppe.par')

Promenade
10-05-17, 02:20
If I am not mistaken, dodecad comes for win and linux both. The "win" means the file is for windows. And you will probably need to emulate windows or linux on your mac in order for it to work

Thank you Aha! I will try that out

Dibran
10-05-17, 02:41
Yes, it works with v4.
This message of error showed up because the Hamit.txt was not found. You have to put it into the folder 'SteppeK10' (in the example), i.e., together the files you downloaded. See below.

I did exactly that though....Which is why I am asking the question.

8665

Regio X
10-05-17, 04:02
I did exactly that though....Which is why I am asking the question.

8665Oh! I see! You put it into "Program File (x86)". Possibly it has something to do with the Admin permission. Try to run R as Admin (right click on the icon, then choose "run as administrator"), and do the steps again.
Other alternative: put SteppeK10 into the C root folder (C:/SteppeK10).

Dibran
10-05-17, 04:40
Oh! I see! You put it into "Program File (x86)". Possibly it has something to do with the Admin permission. Try to run R as Admin (right click on the icon, then choose "run as administrator"), and do the steps again.
Other alternative: put SteppeK10 into the C root folder (C:/SteppeK10).

Tried first by running as administrator(no success).

Moved file to root folder(no success).

Same error.

Dibran
16-05-17, 06:33
Someone was kind enough to run it for me and my father.


Me:

51.57% Near_Eastern
0.00% East_Asian
0.93% Siberian
0.00% Oceanian
23.93% WHG-UHG
0.01% Sub-Saharan
3.59% Hindu_Kush
19.96% Steppe
0.00% Amerindian
0.00% Southeast_Asian


My Father:

50.04% Near_Eastern
0.16% East_Asian
1.12% Siberian
0.00% Oceanian
23.29% WHG-UHG
0.00% Sub-Saharan
5.67% Hindu_Kush
19.35% Steppe
0.36% Amerindian
0.00% Southeast_Asian

New Englander
17-05-17, 02:02
Population



South Asian
1.82


Caucasus
24.79


Southwest Asian
11.78


North Amerindian + Arctic
0.46


Siberian
-


Mediterranean
26.04


East Asian
-


West African
0.12


East European
10.56


North Atlantic
24.43

Syky
21-05-17, 16:21
My results compared to average of other Czech samples from the spreadsheet:



ID
Me
Czech AVG


Near_Eastern
30.85%
29.92%


Steppe
28.15%
29.17%


Hindu_Kush
1.24%
1.68%


WHG-UHG
37.10%
37.64%


East_Asian
0.28%
0.26%


Sub-Saharan
0.00%
0.01%


Oceanian
0.17%
0.28%


Siberian
1.09%
0.34%


Amerindian
1.02%
0.38%


Southeast_Asian
0.09%
0.32%



I am always the most "Amerindian" sample from Czechs... where is the problem? :thinking: