The Italian Genome-Fiorito et al 2015

[Hauteville]

I don't think anyone has pointed out some of the possible reasons for the different placement of the samples, particularly those from Armenia and Turkey, compared to other PCAs with which we're all familiar.

I agree, i don't know why but the positions of Armenians and Turks is radically different from many other PCAs like the one by Lazaridis or the many available on Eurogenes. Like this one.

 

[Angela]

I agree, i don't know why but the positions of Armenians and Turks is radically different from many other PCAs like the one by Lazaridis or the many available on Eurogenes. Like this one.

Fiorito et al doesn't have enough West Asian populations: there are no Iranians, Kurds, no Caucasians like the Adyghe, Lezghins, Abkhasians, no Iraqis etc. The addition or lack of certain populations makes a big difference and significantly changes where certain groups land in relationship to the others, as does which samples are used from which areas and therefore which data set is used.

Lazaridis et al make that point in their supplement. There's a whole section starting on page 76 entitled "Why do our PCAs correlate so poorly to geographic maps of Europe?" They could have added, Why did Novembre et al and some other studies produce PCAs that match that map while we don't? It seems to be that the PCAs that do match the map were made using Popres samples. Those that don't use them are different, including Lazaridis, Skoglund, and Behar.

After an extensive analysis, " We conclude that the pattern of two discontinuous clines that we observe is not an artifact of genotyping errors in the Human Origins data set. At the same time, these analyses highlight how sensitive PCA is to the specific geographic distributions of samples used. Thus, while PCA can be used to suggest interesting hypotheses about history, PCA results are not always unambiguously interpretable in terms of history, and need to be complemented by other types of analyses to produce convincing inferences. In this context, it is crucial that the cline of ancestry proportions that we measure in this study (S114 and S117) is inferred based on analyses that do not depend on the relatiave representation of different regions (as does PCA)."
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4170574/

If I had to go with one PCA I'd go with either the Lazaridis one or the Behar one.

That's why grand theories or pronouncements can't, in my opinion, be drawn simply from one PCA, and why I felt it important to highlight, in post # 100 the different perspective provided by the FST numbers, and also to mention that certain samples might not be very representative of a country or even a region as a whole. Then, as I also mentioned in that post, PCAs don't capture very much of the total genetic variation.

 

[Danelaw]

Those bidimensional plot are often misleading. They simply can't represent all the diversity. The Armenians score two times more of the Druze/Red Component than Sicilians/Calabrians on k=5, so the plot can't be right. What I see is that the software is pushing MENA groups with less SSA towards Europeans. My two cents.

 

[Sile]

wrong thread

 

[Danelaw]

Obviously the plot is representing all the diversity alongside the first axis of SSA vs non SSA admixed populations. The authours should have made a PCA plot without SSA admixed populations like Arabs and Berbers.

 

[Alan]

Fiorito et al doesn't have enough West Asian populations: there are no Iranians, Kurds, no Caucasians like the Adyghe, Lezghins, Abkhasians, no Iraqis etc. The addition or lack of certain populations makes a big difference and significantly changes where certain groups land in relationship to the others, as does which samples are used from which areas and therefore which data set is used.

Lazaridis et al make that point in their supplement. There's a whole section starting on page 76 entitled "Why do our PCAs correlate so poorly to geographic maps of Europe?" They could have added, Why did Novembre et al and some other studies produce PCAs that match that map while we don't? It seems to be that the PCAs that do match the map were made using Popres samples. Those that don't use them are different, including Lazaridis, Skoglund, and Behar.

After an extensive analysis, " We conclude that the pattern of two discontinuous clines that we observe is not an artifact of genotyping errors in the Human Origins data set. At the same time, these analyses highlight how sensitive PCA is to the specific geographic distributions of samples used. Thus, while PCA can be used to suggest interesting hypotheses about history, PCA results are not always unambiguously interpretable in terms of history, and need to be complemented by other types of analyses to produce convincing inferences. In this context, it is crucial that the cline of ancestry proportions that we measure in this study (S114 and S117) is inferred based on analyses that do not depend on the relatiave representation of different regions (as does PCA)."
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4170574/

If I had to go with one PCA I'd go with either the Lazaridis one or the Behar one.

That's why grand theories or pronouncements can't, in my opinion, be drawn simply from one PCA, and why I felt it important to highlight, in post # 100 the different perspective provided by the FST numbers, and also to mention that certain samples might not be very representative of a country or even a region as a whole. Then, as I also mentioned in that post, PCAs don't capture very much of the total genetic variation.

2 dimensional PCA's are never reliable, always use fst distances. PCA's depend on the point of view and you will never be able to show the real relationship of populations simply on PCA's

As example Population A is close to B and C to B too. However C is not really genetically related to A but shows significant relationship to D which itself is closer to some other distant group. How are you going to show this on 2 dimensional PCA? If you put B close to A automatically you need to hold D and C also close to A. This could work with a 3 dimensional PCA but definitely not 2 dimensional.

Therefore using Fst distance table are the best you can do so far.

 

[Danelaw]

From Supp Data

"HIgh IBD between NW Africa and Italy
South Italy(inclu. Sardinia) gets extremly high IBD with NW Africa, suggesting NW African ancestry.
Although other Italians also get much higher IBD with NW Africa than with West Asia, much of it is .25+
If anything this points towards European ancestry in NW Africa."

 

[Pax Augusta]

IBD states, Fiorito 2015

The IBD variation in Italy seems too simple. Almost everything follows a geographic pattern, and it's most North-South.

The highlights for IBD Italy-West Eurasia are.....

.High IBD between NW Africa and South Italy.
.High IBD between North Europe and North Italy.
.High IBD between NE Europe and Basilicata
.Low IBD between West Asia and Italy.

The Highlights for IBD Italy-Italy are....

.NE Italy and Central Italy share a lot of IBD. Variation within the two regions also follow geography, they share the most with their nearest neighbors.
.Some of NE Italy shares a lot of IBD with South Italy.
.South Italy for the most part shares most IBD with each other.

Emilia-Romagna is North Italy in every possible sense, it's not Central Italy.

 

[Mars]

Emilia-Romagna is North Italy in every possible sense, it's not Central Italy.

Yes, absolutely. I noticed that some italian institutions, like ISTAT etc., increase confusion about that: they often put Emilia-Romagna in "central Italy", which is a macroscopic non sense.

 

[Angela]

Razib Khan was late to the party this time. This is his review of Fiorito et al:

http://www.unz.com/gnxp/italy-from-...oot&utm_source=twitterfeed&utm_medium=twitter

http://www.nature.com/ejhg/journal/vaop/ncurrent/abs/ejhg2015233a.html

Of course, he had to pick a picture of Claudia Cardinale wearing very exotic Middle Eastern kohl type make up and a sari to illustrate Italians.

Is this some sort of disorder? Practically the first words I hear when meeting Greeks is "una faccia una razza", or, we look alike, so we're one race. Lebanese and northwestern Turks, even my hairdresser (!), whip out pictures and ask me if their family doesn't look Italian. Same with a Georgian woman who worked as my nanny for a while, and now this. It's all very flattering, but, other than sometimes in the case of the Greeks, the people pointed out to me don't, in the vast majority of cases, look Italian, and that most especially applies to Indians.

 

[Danelaw]

Razib Khan is OWDer with nazi feelings. Unz is blog good for laughs.

 

[Angela]

Razib Khan is OWDer with nazi feelings. Unz is blog good for laughs.

That was totally unnecessary. Razib Khan is a very bright and very well read guy, and his blog is very informative and sensible on a whole raft of issues. He's in no way a Nazi. Leave it to you to take some gentle teasing and turn it into something totally insulting. I neither thought nor meant to imply anything like that. As I said, even though I often don't agree, it's flattering.

Cut it out.

 

[Hauteville]

The worst part are some stormfronter replies in Razib Khan's post imo

 

[Fire Haired14]

Of course, he had to pick a picture of Claudia Cardinale wearing very exotic Middle Eastern kohl type make up and a sari to illustrate Italians.

That's the picture on her Wikpedia page. Probably why Razib chose it.

Is this some sort of disorder? Practically the first words I hear when meeting Greeks is "una faccia una razza", or, we look alike, so we're one race. Lebanese and northwestern Turks, even my hairdresser (!), whip out pictures and ask me if their family doesn't look Italian. Same with a Georgian woman who worked as my nanny for a while, and now this. It's all very flattering, but, other than sometimes in the case of the Greeks, the people pointed out to me don't, in the vast majority of cases, look Italian, and that most especially applies to Indians.

If America was colonized by Middle Easterners and there were Italians and Germans immigrants, I'm sure Germans would say to Italians "You just like us". Anyways, Mexican kids at my school have said "Italians look Mexican". A combination of generic Caucasoid features with a tan complexion=anything from Armenian to Mexican.

and that most especially applies to Indians.

LOL.

 

[Angela]

That's the picture on her Wikpedia page. Probably why Razib chose it.

Well, goodness knows who chose it, because it's not very representative of her. When you google her, these are the first two pictures that come up.

I find her very beautiful, and Sophia Loren as well.

However, there's a lot of variety in Italy, even in the south; these women are just as Italian, and Sicilian as well:

If you want to go to the center of the country, you can get this...

But also this....

This is a very, very, Tuscan look. You can see it all over paintings of the Italian Renaissance, and later.

People just think in stereotypes because that's what the media portrays, no matter the nationality or ethnic group involved.

@Hauteville,

I didn't see those kinds of comments when I read it. I'll have to check it out. Cretini.

 

[Angela]

All I can say is thumbs up to Razib Khan. Now I'm sorry for teasing about the picture. As I said above, a brilliant guy, and one who goes where the data takes him. I just wish he'd ban these storm front types. Morons, one and all, although the knowledge of Italian history and pre-history even among some of the bloggers and posters pontificating about Italy could be fit into a thimble.

Some wisdom from Razib:

"@Rick

I think that there is now a lot of data that suggests that what initially looked like high levels of residual Early Neolithic Farmer ancestry in all of southern Europe is actually from later migrations of people that carried a lot of a similar ancestry, but were not exactly the same.

where’s the data?"

"Razib Khan

says:


December 7, 2015 at 11:48 pm GMT • 100 Words
The Phoenicians aren’t mentioned by Mr. Khan. Perhaps Phoenician trade and colonization is a separate source of southern Italian genetics? Just a thought.

i write what i write for a reason. read closely: The South Italian groups are enriched with the Mozabites and Moroccans, not groups from the eastern Mediterranean. there is a distinctive aspect to maghrebi genetics which separates them from levantines. the south italian samples have that. (there are druze, syrians, and palestinians in the data set to check)."

"Razib Khan says:


December 8, 2015 at 8:12 am GMT • 100 Words
It could easily be from later Roman times as well, when it is well known by historians that there were large numbers of slaves and free immigrants from North Africa and the Middle East imported into Rome.

again, the signal does not seem middle eastern but north african, so you can discount large effect of syrians (there are syrian ref pops, weak IBD signal). please read the post and see the figures before you comment. second, i generally discount slaves. yes, some freedman became very successful (e.g. pertinax’s father; since you are a history buff you’ll know who this is), but the preponderance of slaves in antiquity have very low fertility. the slaves on the latifundia in sicily didn’t have it as bad as those in the mines of sardinia, but it wasn’t a good situation…
despite the fact that greek was heavily spoken in much of italy, and there were attested syrians, the genetic exchange is likely for whatever reason to be mostly with north africa. i suspect during the roman period this had to do with the fact that much of n africa was latin speaking, and many 4th century aristocrats had many of their lands and family roots in that area. but if it was due to the roman period i don’t understand why it’s so weak in latium and central italy, where many of these people congregated. i think it’s because the peasantry remained italian, and the cities evaporated with rome’s collapse.
in contrast, the muslims came in larger numbers, and there was more demographic continuity between islamicized cities and the norman polities."

Razib Khan says:


December 9, 2015 at 4:34 am GMT • 100 Words
@L.K
Genetics show there was very little demographic impact as a result of Roman Slavery,
this is a defensible statement. but as i said above, the historical texts are sufficient to also infer this. slaves were last in line during times of want, and many masters did not seem to want small children who were not economically productive. they had very low fertility, and in some parts of the classical world were banned from having children (i assume infanticide would be a solution?).
the slave reproductive rate in the american south seems to be sui generis. even in the carribean and south america their did not keep at replacement.

As I said, extremely well read.

Razib Khan says:

December 7, 2015 at 11:50 pm GMT • 100 Words

@Matt_
Could be that as there are only a few Italian populations in the mix, the drift of each population becomes more relevant and the levels of shared/different ancient ancestry less relevant, and that homogenises relatedness (and/or splits away Sardinian more in their own cluster)? Any extra drift Sardinians have compared to ancient farmers will pushes them away from all populations equally. PCA or ADMIXTURE with lots of populations will look for what systematically differentiates them from one another as a correlated dimension, which will tend to exclude recent drift particular to any population(s). PCA with a few population can’t do that the same way?

same pattern in the pooled PCA above. also, they put otzi in one of the plots. sort of supports your view, but the pops are not really that differentitaed from otzi. it looks more that they’re being pulled diff directions by non-otzi admixture.

• Razib Khan says:
  
  
  December 9, 2015 at 4:47 am GMT
  @Andrew Lancaster
  I recall from some of the first autosomal studies that Italians were often found to be inexplicably similar to both Sephardi and Ashkenazi Jewish populations
  sephardic jews are not a coherent cluster. i know because i’ve looked at hundreds of seph genotypes.
  Agree • Disagree • Tweet
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• Razib Khan says:
  
  December 9, 2015 at 4:47 am GMT
  @Shaikorth
  Barring ancient DNA what kind of additional references could be added though
  you said it, i didn’t. ancient DNA.
  
  

I could have written these things myself. Heck, I have written them myself. Amazing what an ability to actually interpret data, and interpret it objectively, and a well read mind can do.

 

[Hauteville]

in contrast, the muslims came in larger numbers, and there was more demographic continuity between islamicized cities and the norman polities."

Lol so according to him we are a bunch of transplanted moors, maybe he has read the history in some american historians with multicultural fetish myth because the situation was radically different and the muslims were actually forced to emigrate.

PS: there was never a massive migrations of muslims into Sicily let alone in the mainland regions.

From "CITT?, TERRITORIO, POPOLAZIONE NELLA SICILIA MUSULMANA. UN TENTATIVO DI LETTURA DI UN’EREDIT? CONTROVERSA" by Federico Cresti. Page 31 and 32.

"sulla base delle informazioni disponibili Francesco Gabrieli ha escluso che ci sia mai stata una forte immigrazione dalle coste africane, e anzi ha spiegato la lentezza della conquista con l’esiguit? delle forze impiegate per le spedizioni e per il controllo dell’isola"

Which means: "based on the information available Francesco Gabrieli has excluded that there has ever been a strong immigration from North Africa, and indeed explained the slow pace of conquest with the smallness of the forces involved in the shipments and for control of the island"

 

[frontiersman]

where are the distances in FSTs?

 

[Danelaw]

In the supplementary tables.

 

[Angela]

Lol so according to him we are a bunch of transplanted moors, maybe he has read the history in some american historians with multicultural fetish myth because the situation was radically different and the muslims were actually forced to emigrate.

PS: there was never a massive migrations of muslims into Sicily let alone in the mainland regions.

From "CITT�, TERRITORIO, POPOLAZIONE NELLA SICILIA MUSULMANA. UN TENTATIVO DI LETTURA DI UN’EREDIT� CONTROVERSA" by Federico Cresti. Page 31 and 32.

"sulla base delle informazioni disponibili Francesco Gabrieli ha escluso che ci sia mai stata una forte immigrazione dalle coste africane, e anzi ha spiegato la lentezza della conquista con l’esiguit� delle forze impiegate per le spedizioni e per il controllo dell’isola"

Which means: "based on the information available Francesco Gabrieli has excluded that there has ever been a strong immigration from North Africa, and indeed explained the slow pace of conquest with the smallness of the forces involved in the shipments and for control of the island"

I doubt that he means that there was a large input. You can tell by yDna and mtDna studies that it's not.

The Busby et al study is bunk in a lot of ways.