admixtools2 TUTORIAL for WINDOWS.

I ran your model but the p-values are very low, the reference samples are not very good for those Albanian samples. I've noticed in the past that AV1 and AV2 are hard to make them work.

This is the model with the best p-value, but it is still very low p-value=0.0271, way below the 5% treshold.

Thanks a lot!
It seems formal stats is a totally different world results wise to G25 or PCAs, as expected.
I tried using these samples as proxy for rumored future samples simply because they might overlap on a PCA. But it seems PCA means jack to f2 here. So despite POP_CA possibly overlapping with IA_Albania, there is nothing to it, and in fact samples that don't overlap, possibly later BA-IA ones will yield a better p-value.

Really appreciate you trying to help me sort this out, you showed great patience.
 
Thanks a lot!
It seems formal stats is a totally different world results wise to G25 or PCAs, as expected.
I tried using these samples as proxy for rumored future samples simply because they might overlap on a PCA. But it seems PCA means jack to f2 here. So despite POP_CA possibly overlapping with IA_Albania, there is nothing to it, and in fact samples that don't overlap, possibly later BA-IA ones will yield a better p-value.


Did you fix the error?

Your original path was the correct one, did you correct it?
 
I don't know what's going on with my inbox but I am almost 100% sure it's a path issue, the command cannot find the .geno file.

Based on where you said the .geno file is located on your pc, your path should be C:/Users/xyz/Desktop/fstats/ReichData/v50.0_1240K _public
 
Eupator, I'm such a noob mate.
So when I was supposed to grab all the files from the Reich site? I grabbed just the .geno... so my path had no other documents but the geno. L M A O
 
Yeah, you need all the files. First time for everything.
 
Yeah, you need all the files. First time for everything.

IfksVlY.png


Yep, that se is huge, the model definitively needs those new samples to come out. Albania IA, Vranas Marathon, and hopefully a better Slavic proxy than Avar2.
Thanks for helping me out bro.

Edit: Also, repeating what I said after I saw what results your run yielded before I could get it to work. Overlap on a PCA really means nothing to formal stats.
 
No worries, good job making it work.

You will find out that a lot of models that are taken for granted do fail miserably.

By the way, you can find details about your samples in the .anno file, like place of origin, haplogroup, study that the reference was taken from, etc.

The HO files have more Albanian references, those 2 .DG files are hard to model I remember.
 
Also, overkill right lists can cause really high s.e.

Some people suggest to keep it 15 and below, your mileage will vary.
 
The Marathon sample was probably more East Med compared to most of Mainland Greece as it was in Attica.
 
The Marathon sample was probably more East Med compared to most of Mainland Greece as it was in Attica.

Something something, whispers in the wind are that the East Med outliers / shift should be Dodecanese like. I went ahead and found out what overlaps with Dodecanese to use as a proxy, in essence C4 samples from Italy. But the logic was flawed, since it seems overlapping on the PCA does mean absolutely nothing.
If I knew how to code in R I would make an algo to take from three lists of samples one for the Balkan component, one for the East Med and one for the Slavic, pop the results then rank them based on lowest p-value to the model. To check which combo works as a statistical model.
But at the end of the day it seems that when using populations that share common drift, f2 at least, but from what I hear all qpADM, suffers. Meaning the 3 populations you use could have been ancestral, thus the de facto right model should be built with them, but in reality due to shared ancestry from the three pops, the model would fail.
This could have been the very reason they used Ingria_IA to model Slavic ancestry in the Balkans, lol. Cause otherwise the models would have had horrible, random fits.
 
Yes, someone should inform Reich to switch over to g25, ffs, I mean all the cool kids in the 'east med' gang are using it, wtf does he need qpAdm for.
 
Also, I'd like a definition of the 'east med' terminology so I can understand wtf is the highbrow gang going on about, it seems everything from Abkhazia all the way to Cairo could be labelled as such, according to them.
 
Yes, someone should inform Reich to switch over to g25, ffs, I mean all the cool kids in the 'east med' gang are using it, wtf does he need qpAdm for.

In case my comment was perceived in that light. I also mentioned how G25 or most PCA based models led me astray. In this instance I decided to use the proxies I used just because they supposedly overlap on a PCA, namely G25. But it seems the overlap meant absolutely jack. So I did take a jab at G25 with my previous comment.

As for the East Med, first time I encountered the term was in Antonio et al or was it in the Etruscans 2000yo paper... Ever since, they have made an appearance on 2-3 Balkan papers. So I do think the term is here to stay. Even the Reich Database has some of the samples labeled as "East_Med / East_Med_o".

I would hate to get into fora politics, that's not me, and a waste of time imo.
 
It wasn't directed to you, but towards certain highbrow'ers who constantly obsess over what I do and write on various platforms (by their own admission).

I assume that the 'east med' coinage refers to similarity to Dodecanesians and Cretans, among other closely plotting groups, on their PCAs.

The sad story (for them) is that those Dodecanesian/Cretan "references" do not actually exist anymore in reality (just like Greek_Macedonia) but rather as fringe diaspora entities and imaginary surviving populations of antiquity, and that is due to historical processes and modern intra-regional mobility and inter-mixing of populations within the country.

The Aegean islands were repopulated several times during the Medieval, for Crete specifically we have extensive historical records of how the native population of the time (Saracens and "Greeks" as in Pagans) was almost entirely wiped out (in 960 A.D.) by the Nicephoros Phocas reconquista, down to the last woman and child, and the island repopulated extensively with Pontics, Laz, Armenians, Anatolians, converted Saracen defenders and Balkan Varangian Rus. I dare the highbrow gang to try and challenge the validity of this historical accord.

As such, the Cretans being 'east med' and all, and plotting where they do, is due to the sum of their parts on a PCA and not because they represent an ancestral Med population like they are portrayed.

As for g25, here are my co-ordinates,

eptr_scaled,0.106994,0.139128,-0.017348,-0.031008,0.003077,-0.015618,0.004935,0.002308,-0.022907,0.005103,0.003085,0.002698,-0.011447,0.011973,-0.015472,-0.005701,0.007041,0.00114,0.002514,-0.005002,-0.003369,0.002473,-0.002218,0.003735,-0.003712

And my plot, for those who can't be bothered:
Distance to:eptr_scaled
0.03128242Greek_Crete
0.03565463Greek_Izmir
0.03690988Greek_South_Tsakonia
0.03728822Greek_Deep_Mani
0.03749018Greek_Kos
0.03863699Greek_North_Tsakonia
0.04089436Greek_Dodecanese
0.04094249Italian_Basilicata
0.04111512Greek_East_Taygetos
0.04114372Greek_Laconia
0.04187206Italian_Apulia
0.04252525Greek_Elis
0.04258062Italian_Molise
0.04277087Greek_Central_Anatolia
0.04298084Italian_Calabria
0.04345173Italian_Campania
0.04364641Ashkenazi_Lithuania
0.04385056Greek_Argolis
0.04391181Ashkenazi_Russia
0.04395004Greek_Arcadia
0.04413027Greek_Messenia
0.04414173Ashkenazi_Belarussia
0.04444838Greek_Corinthia
0.04489849Greek_Peloponnese
0.04523358Greek_West_Taygetos


W/o anyone knowing about the sum of my different parental/maternal parts (that have nothing to do with either the East Med or the results listed) what conclusion can be reached? The same one with the Cretans, and/or the Dodecannese?

What if my bones are dug up and tested 300-400 years from now, what would be the future highbrow enthusiast's profession (who constantly neglects all historical and ethnographic data)? That the Levantine 'East Med' invaded the north of Greece in the late 20th/early 21st century?

Are we being serious right now?
 
I think references like Greek_Macedonia and Greek_Crete are done for better historical research in those regions and are selected based on pre 20th century ancestry and nobody is doubting that, especially in 21th century these clusters will gradually disappear.

The Aegean islands were repopulated several times during the Medieval, for Crete specifically we have extensive historical records of how the native population of the time (Saracens and "Greeks" as in Pagans) was almost entirely wiped out (in 960 A.D.) by the Nicephoros Phocas reconquista, down to the last woman and child, and the island repopulated extensively with Pontics, Laz, Armenians, Anatolians, converted Saracen defenders and Balkan Varangian Rus. I dare the highbrow gang to try and challenge the validity of this historical accord.
I think several thousand Armenians and other populations did settle but it was not a large scale replacement.
Do you have sources for this?
 
It wasn't directed to you, but towards certain highbrow'ers who constantly obsess over what I do and write on various platforms (by their own admission).

I assume that the 'east med' coinage refers to similarity to Dodecanesians and Cretans, among other closely plotting groups, on their PCAs.

The sad story (for them) is that those Dodecanesian/Cretan "references" do not actually exist anymore in reality (just like Greek_Macedonia) but rather as fringe diaspora entities and imaginary surviving populations of antiquity, and that is due to historical processes and modern intra-regional mobility and inter-mixing of populations within the country.

The Aegean islands were repopulated several times during the Medieval, for Crete specifically we have extensive historical records of how the native population of the time (Saracens and "Greeks" as in Pagans) was almost entirely wiped out (in 960 A.D.) by the Nicephoros Phocas reconquista, down to the last woman and child, and the island repopulated extensively with Pontics, Laz, Armenians, Anatolians, converted Saracen defenders and Balkan Varangian Rus. I dare the highbrow gang to try and challenge the validity of this historical accord.

As such, the Cretans being 'east med' and all, and plotting where they do, is due to the sum of their parts on a PCA and not because they represent an ancestral Med population like they are portrayed.

As for g25, here are my co-ordinates,



And my plot, for those who can't be bothered:



W/o anyone knowing about the sum of my different parental/maternal parts (that have nothing to do with either the East Med or the results listed) what conclusion can be reached? The same one with the Cretans, and/or the Dodecannese?

What if my bones are dug up and tested 300-400 years from now, what would be the future highbrow enthusiast's profession (who constantly neglects all historical and ethnographic data)? That the Levantine 'East Med' invaded the north of Greece in the late 20th/early 21st century?

Are we being serious right now?

Good example. I think the thought experiment you put forward, really points at the problem of anthrogenetics as a whole. Rather what the current models can and can't say for certain. In a sense despite the highly statistical models used, this is very far from a Popper science. Someone good at statistics could fudge the models / frames of reference and claim very outrageous things if they wanted.
But at least in my mind now, the Ingria_IA which I thought was manipulation of data earlier on, has a more pragmatic explanation... simply getting the model to "work" for 5+ different populations. But really, just cause the model didn't fail (hint: it kinda did cause of huge se when it came to some modern pops), I still wonder how far from the truth we are.
 
I think references like Greek_Macedonia and Greek_Crete are done for better historical research in those regions and are selected based on pre 20th century ancestry and nobody is doubting that, especially in 21th century these clusters will gradually disappear.


I think several thousand Armenians and other populations did settle but it was not a large scale replacement.
Do you have sources for this?


1) The fact that the Greek categories (in g25 and elsewhere) are the only ones that are so numerous in those sheets (with Italians too, I guess) and that they refer to a historical snapshot of a period 100+ years past, most of the people with such autosomal profiles born in the early 20th century and long gone, while blatantly ignoring the current demographic reality of the country is a testament to the sheer idiocy of the small group of perpetrators responsible for those reference sheets and their crypto-racism that tries to disassociate the modern Greek profile from its Eastern/Anatolian demographic part through a process that renders the latter invisible.

2) The main historical sources for the Cretan reconquista are Byzantine chroniclers/historiographers Theodosios and Leon Diakonos and the work titled as "De Creta capta"/"Expugnatio Cretae" written in 962/963.

Some excerpts (with my translation):

a) Cretan Pagans and Saracens are used interchangeably throughout the work, often under the umbrella "barbarians", "the liars ... the beasts of the wicked ...", the reconquista being the "the work of the people of Christ ..."

b) "the fall of the Handakan (Heracleion) castle followed by the mass killings of defenders, the elderly, the women and infants ..."

c) "τὴν νῆσον ἐξημερώσας ἅπασαν, Ἀρμενίων τε καὶ Ῥωμαίων καὶ συγκλύδων ἀνδρῶν φατρίας ἐνοικισάμενος", "the whole island domesticated fully, Armenians and Romans and the conjugates of the (army) clans settling (there) ..."

d) Who were comprising the Byzantine armies in the Cretan reconquista? Let's see, according to Constantinus Porphyrogenitus' Chronicles, we have: Bulgarians, Armenians, Varangian Rus, Anatolians as well as Christian Pechenegs, Alans and Cumans.

Happy reading!

3) In case this post of mine escapes their stalking, you can inform the highbrow gang, and their simpleton 'Mainland Greek' supremacist members of Peloponnesian origin, that my invitation still stands: they can engage me in discourse on public platforms, where I am not censored by their idiot buddy mods, on Medieval Greek ethnography and history and its implications for the modern Greek ethnos.
 

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