• Don't want to see ads? Install an adblocker like uBlock Origin or use a Europe-based privacy-friendly browser like Vivaldi or Mullvad.

Comparing Ancient Greek populations to modern Greeks and Italians

Yeah wish it was around when I started. It helped me get my autosomal data in though.
Regarding the p value and null hypothesis, it depends on how an experiment is constructed. In this case for the model to be viable, IIRC, p>0.05 and se<0.05 are the cutoffs.
 
I have a CRAM, VCF, and BAM version of my Nebula WGS 30x personal DNA sample, how can I read it in ADMIXTOOLS:

This is what ChatGPT told me:

To use a VCF file with `AdmixTools`, you generally need to convert it into a format that `AdmixTools` can process. `AdmixTools` primarily works with EIGENSTRAT format, which consists of a `.snp`, `.ind`, and `.geno` file.


Here's a general outline of the steps you'd follow to get your VCF data ready for `AdmixTools`:


1. **Convert VCF to PLINK format**:
Use `PLINK` to convert the VCF file to PLINK binary format (`.bed`, `.bim`, and `.fam` files).
```bash
plink --vcf yourdata.vcf --make-bed --out yourdata
```


2. **Convert PLINK format to EIGENSTRAT format**:
Use the `convertf` tool from `AdmixTools` to convert the PLINK format data to EIGENSTRAT format. You'll first need a parameter file for `convertf`. Here's an example of what the parameter file (e.g., `par.PED.EIGENSTRAT`) might look like:


```
genotypename: yourdata.bed
snpname: yourdata.bim
individname: yourdata.fam
outputformat: EIGENSTRAT
genotypeoutname: yourdata.geno
snpoutname: yourdata.snp
indivoutname: yourdata.ind
```


Then, run `convertf`:


```bash
convertf -p par.PED.EIGENSTRAT
```


3. **Use EIGENSTRAT data with `AdmixTools`**:
Once you have the `.geno`, `.snp`, and `.ind` files in EIGENSTRAT format, you can use them as input for various `AdmixTools` analyses.


Remember, these steps are a simplification and might require additional parameters or considerations based on the specifics of your data and the goals of your analysis. Always ensure you've done quality control on your VCF data before any downstream analyses, and familiarize yourself with the documentation and options of tools like `PLINK` and `AdmixTools` to make sure you're using them correctly.
 
I converted the VCF to the right formats in PLINK, for EIGENSOFT to convert it to work with Admixtools. Now I just need to install and learn EIGENSOFT. Once I do that, I will be able to model myself in qpadm.
 
Jovialis said:
Yes I think that is right, to get a more perfect score, something else would be needed. Nevertheless, I think this is a good baseline to work off of.
Click to expand...

The score is far from perfect, its not even close to passing. Thats because you need an Armenian like proxy together with the Minoan one or remove minoan and just add the Imperial West Anatolian cluster + North African + Italic.

These are the ID's. Group them.

Code: 
Greek_Rome_Imperial+Mugla(West_Anatolian_Profile),0.1087389,0.1527357,-0.0335888,-0.0700049,0.0004309,-0.0225901,0.0002193,-0.0049076,-0.0057949,0.0243225,0.0046767,0.0034469,-0.0066204,0.0031103,-0.0139793,-0.0054362,0.0047721,0.0004729,0.0040811,-0.0070116,-0.0044421,0.0023824,-0.0023993,0.0029722,0.0008222



TUR_Aegean_Mugla_Camandras_Dalagöz_Rom:I20000,0.114961,0.151314,-0.035826,-0.067184,-0.001231,-0.017291,-0.00047,-0.007154,-0.005113,0.023326,-0.00406,0.007943,-0.009663,0.008395,-0.011265,0.002784,0.0103,-0.00266,0.003897,-0.00988,-0.000125,0.003833,-0.006409,0.001446,0.002155
TUR_Aegean_Mugla_Camandras_Dalagöz_Rom:I20001,0.105855,0.153345,-0.039975,-0.079458,0.000308,-0.01757,-0.012456,-0.010615,-0.004909,0.023326,0.007307,0.005545,-0.010109,0.000688,-0.015744,-0.013126,-0.0103,0.00228,0.01081,-0.01138,-0.00287,-0.000989,0.001109,0.003856,0.008382
TUR_Aegean_Mugla_Camandras_Dalagöz_Rom:I20139,0.110408,0.152329,-0.045632,-0.070414,-0.003077,-0.024821,0.00564,-0.007154,-0.001636,0.014397,0.004709,-0.001948,-0.004757,0.006881,-0.019001,0.002652,0.005737,0.008488,0.005531,-0.014132,-0.00262,0.001237,0.007641,-0.003133,0.000239
ITA_Rome_Imperial:R66,0.111547,0.158423,-0.033187,-0.06783,0.002154,-0.026216,0.00094,-0.002538,-0.013703,0.025331,0.012991,-0.004196,-0.001041,0.00523,-0.022937,-0.014983,-0.005867,0.000507,0.004902,-0.015257,-0.005241,0.00272,-0.003451,0.00253,0.000958
ITA_Rome_Imperial:R71,0.10927,0.158423,-0.044123,-0.068153,-0.003693,-0.029841,0.001645,-0.00923,-0.013294,0.022051,0.001949,0.002698,-0.014123,0.003853,-0.020087,-0.011005,0.009648,0.002407,0.002137,0.005503,-0.004866,-0.00643,0.002588,0.007591,-0.003473
ITA_Rome_Imperial:R72,0.113823,0.145221,-0.033564,-0.073321,-0.003693,-0.030957,0.008695,-0.008538,-0.005931,0.028976,0.009256,0.005545,0.002676,0.002202,-0.010315,-0.002254,0.007432,0.002027,0.005908,-0.002501,0.000749,0.002968,-0.008504,-0.001566,0.006107
ITA_Rome_Imperial:R78,0.113823,0.157407,-0.031301,-0.079458,0.002154,-0.03012,-0.000705,-0.007846,-0.007772,0.019317,0.002436,0.005095,-0.009366,0.008395,-0.013436,-0.017369,-0.002217,0.000253,0.010936,-0.006503,-0.007237,-0.000989,-0.006286,-0.000482,0.005389
ITA_Rome_Imperial:R81,0.108132,0.15436,-0.026398,-0.063308,0.005232,-0.027052,0.000705,0.008307,-0.001432,0.025149,0.005521,-0.003897,-0.002825,-0.005367,-0.010315,-0.001989,0.012126,0.004307,0.008422,0.001501,-0.010856,0.001484,0.00419,-0.001205,-0.001197
ITA_Rome_Imperial:R40,0.105855,0.151314,-0.023004,-0.060078,0.001539,-0.013666,-0.00141,-0.004846,-0.012067,0.027882,0.007307,0.003447,-0.010555,0.000275,-0.017236,-0.000796,0.000261,-0.00076,-0.002388,-0.01113,-0.004742,0.000371,-0.013188,0.004338,-0.000359
ITA_Rome_Imperial:R41,0.095611,0.139128,-0.036204,-0.076551,0.004924,-0.026216,-0.00282,-0.005769,0.002863,0.023508,0.003248,-0.001199,0.001635,0.004404,-0.006379,0.000796,0.002347,-0.003294,-0.001634,-0.005503,-0.005989,0.000866,0.00037,-0.001205,0.003952
ITA_Rome_Imperial:R43,0.111547,0.153345,-0.032809,-0.067184,0.003693,-0.025379,0.00423,-0.006,-0.007976,0.029704,0.003248,0.011839,-0.014717,0.006881,-0.017101,-0.000663,0.017341,0.003167,0.005028,-0.000625,-0.010981,0.010881,-0.003204,0.010001,-0.00012
ITA_Rome_Imperial:R44,0.117238,0.167562,-0.028284,-0.070737,0.004616,-0.019522,0.001175,-0.006692,-0.003886,0.034807,0.006333,0.008243,-0.013379,0.001651,-0.009229,-0.004508,0.017211,-0.00038,-0.003268,-0.007003,-0.000873,0.000618,0.001479,0.008314,0.001437
ITA_Rome_Imperial:R1545,0.105855,0.153345,-0.032809,-0.065569,0.001231,-0.016733,-0.00141,-0.000923,-0.006136,0.019864,0.002436,0.003597,-0.007136,-0.000275,-0.015472,-0.015911,-0.008214,-0.002027,0.005028,-0.007629,0.000499,0.011747,-0.005176,0.005784,-0.007065
ITA_Rome_Imperial:R126,0.101303,0.150298,-0.038466,-0.074936,-0.005847,-0.020917,-0.00235,-0.007154,-0.003681,0.027882,0.004872,0.002698,-0.000892,0.001514,-0.009772,-0.003447,0.00665,-0.006968,0.002263,-0.009004,-0.004367,0.003091,-0.003328,0.003615,-0.00012
ITA_Rome_Imperial:R115,0.105855,0.145221,-0.02225,-0.065892,-0.001846,-0.01255,0.00188,0.002538,-0.00225,0.019317,0.002598,0.006294,-0.005054,0.001927,-0.011401,-0.001724,0.009127,-0.000253,0.003645,-0.011631,-0.007112,0.004328,-0.003821,0.004699,-0.003952
 
The model does not seem to improve when using Eastern Mediterranean samples from Rome in qpADM.
 
Idontknowwhatimdoing said:
The score is far from perfect, its not even close to passing. Thats because you need an Armenian like proxy together with the Minoan one or remove minoan and just add the Imperial West Anatolian cluster + North African + Italic.

These are the ID's. Group them.

Code: 
Greek_Rome_Imperial+Mugla(West_Anatolian_Profile),0.1087389,0.1527357,-0.0335888,-0.0700049,0.0004309,-0.0225901,0.0002193,-0.0049076,-0.0057949,0.0243225,0.0046767,0.0034469,-0.0066204,0.0031103,-0.0139793,-0.0054362,0.0047721,0.0004729,0.0040811,-0.0070116,-0.0044421,0.0023824,-0.0023993,0.0029722,0.0008222



TUR_Aegean_Mugla_Camandras_Dalagöz_Rom:I20000,0.114961,0.151314,-0.035826,-0.067184,-0.001231,-0.017291,-0.00047,-0.007154,-0.005113,0.023326,-0.00406,0.007943,-0.009663,0.008395,-0.011265,0.002784,0.0103,-0.00266,0.003897,-0.00988,-0.000125,0.003833,-0.006409,0.001446,0.002155
TUR_Aegean_Mugla_Camandras_Dalagöz_Rom:I20001,0.105855,0.153345,-0.039975,-0.079458,0.000308,-0.01757,-0.012456,-0.010615,-0.004909,0.023326,0.007307,0.005545,-0.010109,0.000688,-0.015744,-0.013126,-0.0103,0.00228,0.01081,-0.01138,-0.00287,-0.000989,0.001109,0.003856,0.008382
TUR_Aegean_Mugla_Camandras_Dalagöz_Rom:I20139,0.110408,0.152329,-0.045632,-0.070414,-0.003077,-0.024821,0.00564,-0.007154,-0.001636,0.014397,0.004709,-0.001948,-0.004757,0.006881,-0.019001,0.002652,0.005737,0.008488,0.005531,-0.014132,-0.00262,0.001237,0.007641,-0.003133,0.000239
ITA_Rome_Imperial:R66,0.111547,0.158423,-0.033187,-0.06783,0.002154,-0.026216,0.00094,-0.002538,-0.013703,0.025331,0.012991,-0.004196,-0.001041,0.00523,-0.022937,-0.014983,-0.005867,0.000507,0.004902,-0.015257,-0.005241,0.00272,-0.003451,0.00253,0.000958
ITA_Rome_Imperial:R71,0.10927,0.158423,-0.044123,-0.068153,-0.003693,-0.029841,0.001645,-0.00923,-0.013294,0.022051,0.001949,0.002698,-0.014123,0.003853,-0.020087,-0.011005,0.009648,0.002407,0.002137,0.005503,-0.004866,-0.00643,0.002588,0.007591,-0.003473
ITA_Rome_Imperial:R72,0.113823,0.145221,-0.033564,-0.073321,-0.003693,-0.030957,0.008695,-0.008538,-0.005931,0.028976,0.009256,0.005545,0.002676,0.002202,-0.010315,-0.002254,0.007432,0.002027,0.005908,-0.002501,0.000749,0.002968,-0.008504,-0.001566,0.006107
ITA_Rome_Imperial:R78,0.113823,0.157407,-0.031301,-0.079458,0.002154,-0.03012,-0.000705,-0.007846,-0.007772,0.019317,0.002436,0.005095,-0.009366,0.008395,-0.013436,-0.017369,-0.002217,0.000253,0.010936,-0.006503,-0.007237,-0.000989,-0.006286,-0.000482,0.005389
ITA_Rome_Imperial:R81,0.108132,0.15436,-0.026398,-0.063308,0.005232,-0.027052,0.000705,0.008307,-0.001432,0.025149,0.005521,-0.003897,-0.002825,-0.005367,-0.010315,-0.001989,0.012126,0.004307,0.008422,0.001501,-0.010856,0.001484,0.00419,-0.001205,-0.001197
ITA_Rome_Imperial:R40,0.105855,0.151314,-0.023004,-0.060078,0.001539,-0.013666,-0.00141,-0.004846,-0.012067,0.027882,0.007307,0.003447,-0.010555,0.000275,-0.017236,-0.000796,0.000261,-0.00076,-0.002388,-0.01113,-0.004742,0.000371,-0.013188,0.004338,-0.000359
ITA_Rome_Imperial:R41,0.095611,0.139128,-0.036204,-0.076551,0.004924,-0.026216,-0.00282,-0.005769,0.002863,0.023508,0.003248,-0.001199,0.001635,0.004404,-0.006379,0.000796,0.002347,-0.003294,-0.001634,-0.005503,-0.005989,0.000866,0.00037,-0.001205,0.003952
ITA_Rome_Imperial:R43,0.111547,0.153345,-0.032809,-0.067184,0.003693,-0.025379,0.00423,-0.006,-0.007976,0.029704,0.003248,0.011839,-0.014717,0.006881,-0.017101,-0.000663,0.017341,0.003167,0.005028,-0.000625,-0.010981,0.010881,-0.003204,0.010001,-0.00012
ITA_Rome_Imperial:R44,0.117238,0.167562,-0.028284,-0.070737,0.004616,-0.019522,0.001175,-0.006692,-0.003886,0.034807,0.006333,0.008243,-0.013379,0.001651,-0.009229,-0.004508,0.017211,-0.00038,-0.003268,-0.007003,-0.000873,0.000618,0.001479,0.008314,0.001437
ITA_Rome_Imperial:R1545,0.105855,0.153345,-0.032809,-0.065569,0.001231,-0.016733,-0.00141,-0.000923,-0.006136,0.019864,0.002436,0.003597,-0.007136,-0.000275,-0.015472,-0.015911,-0.008214,-0.002027,0.005028,-0.007629,0.000499,0.011747,-0.005176,0.005784,-0.007065
ITA_Rome_Imperial:R126,0.101303,0.150298,-0.038466,-0.074936,-0.005847,-0.020917,-0.00235,-0.007154,-0.003681,0.027882,0.004872,0.002698,-0.000892,0.001514,-0.009772,-0.003447,0.00665,-0.006968,0.002263,-0.009004,-0.004367,0.003091,-0.003328,0.003615,-0.00012
ITA_Rome_Imperial:R115,0.105855,0.145221,-0.02225,-0.065892,-0.001846,-0.01255,0.00188,0.002538,-0.00225,0.019317,0.002598,0.006294,-0.005054,0.001927,-0.011401,-0.001724,0.009127,-0.000253,0.003645,-0.011631,-0.007112,0.004328,-0.003821,0.004699,-0.003952
Click to expand...

sODMvmg.png


7VoasCJ.png


The results suggest Armenian should be excluded.
 
Jovialis said:
sODMvmg.png


7VoasCJ.png


The results suggest Armenian should be excluded.
Click to expand...

It doesnt suggest anything, it just suggests the the whole model is bad, you dont know which proxy is not needed in this context.

Whats a good Germanic proxy for Italians on qpAdm?
 
Jovialis said:
sODMvmg.png



The results suggest Armenian should be excluded.
Click to expand...

This model passed but its inflating North Euro stuff because South Italians might need some high steppe Cetina related proxy plus a little bit of Slavic.
wLkYFh5g5L8eQAAAABJRU5ErkJggg==

OzUHLmj.png

Code: 
right = c('Ethiopia_4500BP.DG', 'Morocco_Iberomaurusian', 'Turkey_N', 'Iran_TepeAbdulHosein_N', 'Russia_Samara_EBA_Yamnaya', 'Bichon_WHG', 'China_AmurRiver_LPaleolithic', 'Jordan_PPNB')


left = c('Aegean_Anatolian_Greek_Imperial_Rome_Mugla', 'Italy_Republic_900_600_BC', 'CanaryIslands_Guanche.SG', 'Norwegian')


target = c('Italian_South')


results = qpadm(prefix, left, right, target, allsnps = TRUE)
results$weights
results$popdrop

The right pops though are too old, we should use bronze age right pops when using iron age-roman era left pops. I did in a model and it passed too.
 
Idontknowwhatimdoing said:
Thats because you need to use the proper ones, proper right pops and proper left pops.
Click to expand...

I don't know, frankly, if the East Med samples in Rome isn't sufficient, it is a hard sell for me, considering that's primarily what people point to as the source.


Also, I have never heard of Slavic in Southern Italy. I only remember some guy named sikeliot/azzurro who pushed hard for that. Moreover, Germanic in southern Italy would even be very difficult to demonstrate in the south. The Lombards for example did not leave much of an impact at all on the south.
 
I can give you a tail that worked for me and maybe it improves your models? But its very dependent on what hypothesis you are trying to test, check the paper I shared earlier.

About the plink stuff. The way I did it was by installing a Linux VM, I think I have some details saved, if you want I can PM.
 
Jovialis said:
I don't know, frankly, if the East Med samples in Rome isn't sufficient, it is a hard sell for me, considering that's primarily what people point to as the source.


Also, I have never heard of Slavic in Southern Italy. I only remember some guy named sikeliot/azzurro who pushed hard for that. Moreover, Germanic in southern Italy would even be very difficult to demonstrate in the south. The Lombards for example did not leave much of an impact at all on the south.
Click to expand...

Slavic in South Italy must be Byzantine related.

Germanics definitely left a small impact on South Italy and Sicily, its clear on G25, if its directly or indirectly from North Italians i dont know. The same thing happened in Cyprus, mainland Greeks before 1000 ad moved to Cyprus and brought 1-3% Slavic. So something like that i guess happened in South Italy. Many people get shocked when i tell them that there is some Slavic in Cyprus.

Calabrians, Sicilians only score 5% Germanic. Can you send me what you think are the best G25 Germanic coordinates for Italians, incase the ones i used are bad?

Italians are Graeco-Roman genetically, based.

l6DojpU.png
 
LkmoQUf.png


BuY3iSA.png


Turns out the P-score for my model is indeed closer to 0.05 though.
 
Jovialis said:
LkmoQUf.png


BuY3iSA.png


Turns out the P-score for my model is indeed closer to 0.05 though.
Click to expand...

Your p value is very bad, 9-71e-10 = 0.000000000971. It is not close to 0.05 at all.

Do you know how to read 9-71e-10?

on qpAdm you are not supposed to rank p values yourself. qpAdm theory clealy states that higher p value models are not better, all that matters is that the p value is above 0.05. A p value of 0.000000000971 means that is is impossible for that model to be true. Its missing most of the required proxies.

Italians are simply not a mix of Minoan related + Steppe, They are a mix of Greek West Anatolian + pre-Imperial Italian (which includes some Balkan like stuff) + some excess Levant + North African + Germanic/Slavic.
 
GPT is notably bad at math. It's like 9 orders of magnitude off, x10^-10, you are looking for x10^-1, or ^-2.
5x10^-2 is 0.05, and 5x10-10 is 0.00000000005.
 
Archetype0ne said:
GPT is notably bad at math. It's like 9 orders of magnitude off, x10^-10, you are looking for x10^-1, or ^-2.
5x10^-2 is 0.05, and 5x10-10 is 0.00000000005.
Click to expand...

The math it provided was incorrect in the post?
 
Idontknowwhatimdoing said:
Your p value is very bad, 9-71e-10 = 0.000000000971. It is not close to 0.05 at all.

Do you know how to read 9-71e-10?

on qpAdm you are not supposed to rank p values yourself. qpAdm theory clealy states that higher p value models are not better, all that matters is that the p value is above 0.05. A p value of 0.000000000971 means that is is impossible for that model to be true. Its missing most of the required proxies.

Italians are simply not a mix of Minoan related + Steppe, They are a mix of Greek West Anatolian + pre-Imperial Italian (which includes some Balkan like stuff) + some excess Levant + North African + Germanic/Slavic.
Click to expand...

I'm still pretty new, but what I'm trying to do is replicate what studies have demonstrated.
 
You must log in or register to reply here.
Back
Top