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Angela
09-09-16, 21:09
Using whole-genome sequencing to shed insight on the complex prehistory of Sardinia. Chiang et al

https://ep70.eventpilot.us/web/page.php?page=IntHtml&project=ASHG16&id=160122402

"Abstract:
Genetic studies of complex traits using individuals from the island of Sardinia have been fruitful for decades. Understanding the population history of Sardinia may provide insights to how risk alleles arise in Sardinia and the expected degree of sharing with mainland populations. Current models for the peopling of Europe consider extant Europeans as having varying ancestral contributions from Paleolithic hunter-gatherers, Neolithic farmers, and Steppe pastoralists. In these analyses, extant Sardinians are inferred with the largest amount of Neolithic farmer ancestry among Europeans. However, previous studies of uniparental markers have highlighted the high frequency of the Y-chromosome haplotype I2a1a1 in Sardinia, which has been associated with Paleolithic ancestry in Europe. Here we aim to elucidate finer details of the population history of Sardinia. We study >3,500 whole-genome sequenced individuals across Sardinia together with reference European datasets and recently published ancient humans. We confirm that compared to mainland Europeans, Sardinians exhibit the greatest amount of shared drift with Neolithic farmers. Within the island of Sardinia, there is a demarcation of individuals from the Lanusei Valley in the geographically isolated province of Ogliastra and individuals from other provinces. In unsupervised analyses, a Sardinian-specific ancestry component correlates with shared drift parameters with both the Neolithic farmers and Paleolithic hunter-gatherers, and is consistent with supervised estimates of ancestry proportions in which the Ogliastra individuals have higher Neolithic farmer and Paleolithic hunter-gatherer ancestries, while individuals from the rest of the island show an infusion of the pastoralist ancestry. Finally, we find that the Sardinian people exhibit increased sharing of alleles with the Neolithic farmers on the X chromosome compared to the autosome (P < 1x10-4), suggesting a sex-biased demographic history in Sardinia. Together, our results indicate that in addition to the strong Neolithic farmer component of ancestry, isolated regions of Sardinia also harbors significant ancestry components from Paleolithic Europe and that the Neolithic transition in Sardinia may have involved sex-biased demographic change. These results help provide more insight into the history of Sardinians and the frequency distribution of variants they carry."

It will be interesting to see the differences in Ydna by area.

Other than that, I think we've known this for a while.

This is Ogliasatra:
http://www.edilcostasarda.it/blog/wp-content/uploads/2011/05/ogliastra.jpg


These are the people of Lanusei:
https://s-media-cache-ak0.pinimg.com/236x/16/d7/2d/16d72d77a6eed3a5edf9efa9db853396.jpg



http://farm4.static.flickr.com/3088/2375026490_b87e84b8a3_m.jpg

https://s-media-cache-ak0.pinimg.com/236x/f9/df/84/f9df8445a9e77553d66debc70abcd7fb.jpg

https://i.ytimg.com/vi/NOegu2jgJcY/hqdefault.jpg

http://lanuovasardegna.gelocal.it/polopoly_fs/1.10597050.1420249267!/httpImage/image.jpg_gen/derivatives/detail_558/image.jpg

bicicleur
10-09-16, 06:00
why are they talking about a component of paleolithic Europe?

Sardinia was deserted for almost 2000 years before the first cardial/impressed ware people arrived there

it has to have something to do with those I2a1a1

Fire Haired14
10-09-16, 08:05
"and is consistent with supervised estimates of ancestry proportions in which the Ogliastra individuals have higher Neolithic farmer and Paleolithic hunter-gatherer ancestries, while individuals from the rest of the island show an infusion of the pastoralist ancestry"

"Together, our results indicate that in addition to the strong Neolithic farmer component of ancestry, isolated regions of Sardinia also harbors significant ancestry components from Paleolithic "

This is interesting. Sardinian's with the most Neolithic affinity in Sardinia also having the most Paleolithic affinity in Sardinia makes sense if non-Sardinian admixture is from Southern Italy. It'll be interesting to see how much EEF/WHG Ogliastra has.

Angela
10-09-16, 20:19
why are they talking about a component of paleolithic Europe?

Sardinia was deserted for almost 2000 years before the first cardial/impressed ware people arrived there

it has to have something to do with those I2a1a1

I agree. I think the whole "Sardinian" thing is rather simplistically understood. It's true that Mesolithic remains have been discovered on the island, but there isn't a lot of archaeological evidence for a large population, so I tend to doubt that most of their WHG came from this group. Therefore, it's not, imo, a case of a place inhabited by Mesolithic (not Paleolithic) inhabitants, the arrival of the Neolithic with farmers, and then the curtain sort of drops in the interior areas, at least.

I've thought it might be that in addition to the original Neolithic inhabitants, there was an exodus from the Balkans of those Neolithic groups, basically a mix of EEF and WHG, and they went west, bringing copper metallurgy with them.

They might have carried a lot of I2a1a1. That's why I'm intrigued by the findings of the upcoming Matthiesen paper that central and northern Europeans don't descend from a "Balkan" mix of these groups. Before the paper comes out, maybe they should test the Sardinians as well. Perhaps this is where those people went. That, or groups of mixed Koros Mesolithic and Anatolian Neolithic people back migrated to the Balkans from Central Europe.

Another possibility is that part of the migration was from Neolithic Greece. See the Ozieri culture, dated to about 3200 BC:
https://en.wikipedia.org/wiki/Ozieri_culture

"Some tombs, of more monumental appearance, belonged perhaps to chiefs, in the fashion of those in Crete.Religion has been suggested to have involved the adoration of the Neolithic Mother goddess (https://en.wikipedia.org/wiki/Mother_goddess) and of a Bull god, perhaps connected to fertility. These claims, in recent scholarship, have been called into question on the basis that too much is inferred from too little evidence.[4] (https://en.wikipedia.org/wiki/Ozieri_culture#cite_note-4) Female statuettes similar to those of the Ozieri culture have been found in Malta.[5] (https://en.wikipedia.org/wiki/Ozieri_culture#cite_note-FOOTNOTELilliu196716-5)"

This type of ancestry might have persisted in a lot of areas of southern Europe for a very long time indeed. I think results from running ancient genomes through calculators have to be interpreted very carefully, but didn't one of the Thracian Bronze Age samples
come out as mostly "Mediterranean Islander"?

Interestingly, land ownership in Sardinia was communal until almost into the modern era.

The Arzachena culture which is roughly contemporaneous covered a smaller part of Sardinia and is a little different.

See:https://en.wikipedia.org/wiki/Arzachena_culture
"Both the funerary architecture and the material culture show similarities with contemporary contexts of Catalonia (https://en.wikipedia.org/wiki/Catalonia), Languedoc (https://en.wikipedia.org/wiki/Languedoc),Provence (https://en.wikipedia.org/wiki/Provence) and Corsica (https://en.wikipedia.org/wiki/Corsica).
Differently from the people of the contemporary Ozieri culture (https://en.wikipedia.org/wiki/Ozieri_culture) of the rest of Sardinia, the people of the Arzachena culture were organized in an aristocratic and individualistic society[4] (https://en.wikipedia.org/wiki/Arzachena_culture#cite_note-Lilliu2-4) focused on pastoralism rather than agriculture. The aristocratic groups buried their dead in megalithic monuments in the shape of a circle, with a central chamber containing a single individual,[5] (https://en.wikipedia.org/wiki/Arzachena_culture#cite_note-5) while in the rest of the island the Ozieri people buried their dead in collectivehypogeum (https://en.wikipedia.org/wiki/Hypogeum) tombs called Domus de Janas (https://en.wikipedia.org/wiki/Domus_de_Janas).[4] (https://en.wikipedia.org/wiki/Arzachena_culture#cite_note-Lilliu2-4)"

@Firehaired,
Increasingly, there was migration to Sardinia from northern Italy. I think the U-152 largely came from there and from central Italy as well. It was ceded to the Piemontese House of Savoy in 1718. Prior to that it was part of Aragon and the Spanish crown, when the total decline began. Before that it was battled over by Pisa and Genova. (Certain cities were allied to Genova, certain cities to Pisa). Saracens and Vandals raided coastal cities, the Vandals bringing in African auxiliaries.

That's why conclusions about Sardinian genetics should only be made in consultation with historians who understand the history of the places where the samples were taken. I've been saying this for years. The initial sample for Sardinia was chosen by Cavalli-Sforza, who could never be charged with a lack of historical knowledge about Italy. (He chose Bergamo for North Italy, northeast of Firenze for Toscana, as well.) He took it from Ogliastro, if I remember correctly, or at least some other isolated mountain area, so most of the conclusions about Sardinian genetics have been based on these people, not coastal Sardinians.

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

davef
10-09-16, 20:45
Wow. I always felt that it was simply a bunch of neolithic farmers gathering on an island and drifting off genetically through isolation.

Angela:"This type of ancestry might have persisted in a lot of areas of southern Europe for a very long time indeed. I think results from
running ancient genomes through calculators have to be interpreted very carefully, but didn't one of the Thracian Bronze Age samples
come out as mostly "Mediterranean Islander"?
Interestingly, land ownership in Sardinia was communal until almost into the modern era."

I SAW THAT AS WELL! Maybe the greeks were more southern before later mixing with northerners? Seems likely!

I know drawing comparisons with modern populations using dna land isn't the cats meow but this result is something to think about...

Sorry for straying from the topic

Cato
15-09-16, 19:01
I think that the steppe-like ancestry among Sardinians is actually mostly Pre-historic. Archaeology/Physical anthropology suggest that in the late Copper age and in the early Bronze age people from North/Central Italy and Central Europe settled in Sardinia (curiously not in Ogliastra and most of the eastern coast), archaeologist Giovanni Lilliu speculate that these warrior-shepherds were in part responsable for the birth of the Nuragic civilization, the Bonnanaro culture was in fact strongly related with the Polada culture and the Beaker culture

A good read about this subject is: La civiltà dei Sardi dal Paleolitico all'età dei Nuraghi, 2004

Angela
15-09-16, 19:28
For those who can't read Italian, a short reference can be found to this source of the Nuragic in the Wiki article on the subject:
https://en.wikipedia.org/wiki/Nuragic_civilization

Cato
15-09-16, 20:07
some quotes from the Book (translated with google)


It is perhaps because of stimuli and models (and - why not? - some gush of blood) from the Central European and the Polada-Rhone areas, that the culture of Bonnanaro I gives a jolt to the past and produces in step with the new times


The strong and widespread presence of the Aquitanian-Mediterranean and the Old-Mediterranean types would recognize in these the fundamental ethnic and original substratum of the island, in which, during the age of the Ancient bronze, and perhaps as early as the Chalcolithic, dropped Recent-Mediterranean and Brachymorphic minorities. Especially the minoritarian Brachymorphic group had to be especially rich in technical experiences and ideals stimuli, capable of initiatives and fierce in behavior, so that explains , with it the renewal brought in the Ancient Bronze Age and then continued in the Middle Bronze Age. The group was welcomed, not know with what degree of tolerance, from the majority ethnic substratum.

Sile
15-09-16, 20:15
some quotes from the Book (translated with google)

I do not understand what was meant by Polada -rhone for sardinia

https://books.google.com.au/books?id=h70veOOMgIQC&pg=PA14&lpg=PA14&dq=polada+rhone&source=bl&ots=YFxigqk9_a&sig=YJhqq36XphVYxFgWXMKcsWLRUy0&hl=en&sa=X&ved=0ahUKEwjOpJr27pHPAhVBWWMKHWHFDA8Q6AEIQTAH#v=on epage&q=polada%20rhone&f=false

Polada is from lake Garda Veneto Italy

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

Cato
25-09-16, 18:40
I do not understand what was meant by Polada -rhone for sardinia

https://books.google.com.au/books?id=h70veOOMgIQC&pg=PA14&lpg=PA14&dq=polada+rhone&source=bl&ots=YFxigqk9_a&sig=YJhqq36XphVYxFgWXMKcsWLRUy0&hl=en&sa=X&ved=0ahUKEwjOpJr27pHPAhVBWWMKHWHFDA8Q6AEIQTAH#v=on epage&q=polada%20rhone&f=false

Polada is from lake Garda Veneto Italy

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

The Rhone culture was an early Bronze age culture from Southern France related to that of Polada. They were variants of the Unetice culture together with Straubing, Adlerberg and other groups near the Alps.

Pax Augusta
01-11-16, 14:52
Wow. I always felt that it was simply a bunch of neolithic farmers gathering on an island and drifting off genetically through isolation.

The isolation of Sardinia is overstated. Since Middle Ages there were significant migrations from Corsica, Northern and Central Italy. Of course in Sardinia there are areas more isolated than others.




That's why conclusions about Sardinian genetics should only be made in consultation with historians who understand the history of the places where the samples were taken. I've been saying this for years. The initial sample for Sardinia was chosen by Cavalli-Sforza, who could never be charged with a lack of historical knowledge about Italy. (He chose Bergamo for North Italy, northeast of Firenze for Toscana, as well.) He took it from Ogliastro, if I remember correctly, or at least some other isolated mountain area, so most of the conclusions about Sardinian genetics have been based on these people, not coastal Sardinians.

Angela, are you sure that the 8 people Tuscan HGDP sample is from northeast of Florence? I never found that information. The 1000 genomes/HapMap TSI sample for Tuscans, as I know, is from an unspecified town of the Florentine province.

LABERIA
01-11-16, 15:33
The isolation of Sardinia is overstated. Since Middle Ages there were significant migrations from Corsica, Northern and Central Italy. Of course in Sardinia there are areas more isolated than others.




Angela, are you sure that the 8 people Tuscan HGDP sample is from northeast of Florence? I never found that information. The 1000 genomes/HapMap TSI sample for Tuscans, as I know, is from an unspecified town of the Florentine province.

There are some italian scholars like Salvatore Bovore, Alberto Areddu, etc, who support the theory of the connection between Albanian language and a sardinian dialect spoken in the region of Monte Santo, Barbagia, East Sardegna.
There is not too much information in english about this. This is in italian:
http://www.vatrarberesh.it/argomenti-trattati/la-lingua/arvareshu-il-protosardo-illirico.html

LABERIA
01-11-16, 15:37
Searching in Google i see that this topic has been discussed even here in Eupedia:
http://www.eupedia.com/forum/threads/26476-Alberto-G-Areddu-author-of-the-book-Albanian-Origins-of-Civilization-in-Sardinia%E2%80%9D

I don't know how accurate is this theory, just my two cents.

Angela
01-11-16, 17:42
The isolation of Sardinia is overstated. Since Middle Ages there were significant migrations from Corsica, Northern and Central Italy. Of course in Sardinia there are areas more isolated than others.




Angela, are you sure that the 8 people Tuscan HGDP sample is from northeast of Florence? I never found that information. The 1000 genomes/HapMap TSI sample for Tuscans, as I know, is from an unspecified town of the Florentine province.

Thanks for catching that, Pax. Yes, it's HAP MAP/1000 Genomes/TSI that's from the province of Firenze. I'm pressed for time, so check me, but this site lists the HGDP samples by coordinates.

http://www.cephb.fr/en/hgdp_panel.php.

Click on table and it would seem the Tuscan sample is from 43N 11E, which would be around Tatti, frazione di Massa Marittima, right between Grosseto and Siena? That's about as far south in Toscana as you can go.

https://it.wikipedia.org/wiki/Tatti_(Massa_Marittima)

I wonder what he was looking for? Maybe a more isolated area than that around Firenze? Something near Grotta dello Scoglietto or Etruscan centers?

https://translate.google.com/translate?hl=en&sl=it&u=https://it.wikipedia.org/wiki/Grotta_dello_Scoglietto&prev=search

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

It would be interesting if someone could run both samples through calculators just to see if there are any significant differences.

Pax Augusta
22-12-16, 16:08
Thanks for catching that, Pax. Yes, it's HAP MAP/1000 Genomes/TSI that's from the province of Firenze. I'm pressed for time, so check me, but this site lists the HGDP samples by coordinates.

http://www.cephb.fr/en/hgdp_panel.php. .

Click on table and it would seem the Tuscan sample is from 43N 11E, which would be around Tatti, frazione di Massa Marittima, right between Grosseto and Siena? That's about as far south in Toscana as you can go.

Exactly, according to these coordinates the Tuscan HGDP sample is from Colline Metallifere in the province of Grosseto, so yes, it's about as far south in Tuscany as you can go. Cavalli-Sforza was clearly searching an "Etruscan" sample. Even in Tuscany exists a cline, so HGDP can represent well southern and central Tuscans but not so well the northern Tuscans, especially the northwestern Tuscans. Not by chance they can come out as closer to the northern Italian sample or intermediate between Lombardy and Tuscany.

According to the CEPH V3.0 Database coordinates, the HGDP Bergamo sample is from the Prealps, between Spiazzi and Lizzola, so it's about as far north in Lombardy you can go. Anyway, it's not, genetically speaking, the most northern place in North Italy, which is clearly situated in the northeastern Italian Alps, between Trentino, northern Veneto and Friuli-Venezia-Giulia. While Aosta Valley is clearly the most northwestern area of Italy, genetically speaking.

Last but not least, according to the CEPH V3.0 Database coordinates, the Sardinian HGDP sample is from Barbagia, between Ortueri and Atzara. Barbagia is an isolated area from central Sardinia.

Angela
22-12-16, 18:34
Exactly, according to these coordinates the Tuscan HGDP sample is from Colline Metallifere in the province of Grosseto, so yes, it's about as far south in Tuscany as you can go. Cavalli-Sforza was clearly searching an "Etruscan" sample. Even in Tuscany exists a cline, so HGDP can represent well southern and central Tuscans but not so well the northern Tuscans, especially the northwestern Tuscans. Not by chance they can come out as closer to the northern Italian sample or intermediate between Lombardy and Tuscany.

According to the CEPH V3.0 Database coordinates, the HGDP Bergamo sample is from the Prealps, between Spiazzi and Lizzola, so it's about as far north in Lombardy you can go. Anyway, it's not, genetically speaking, the most northern place in North Italy, which is clearly situated in the northeastern Italian Alps, between Trentino, northern Veneto and Friuli-Venezia-Giulia. While Aosta Valley is clearly the most northwestern area of Italy, genetically speaking.

Last but not least, according to the CEPH V3.0 Database coordinates, the Sardinian HGDP sample is from Barbagia, between Ortueri and Atzara. Barbagia is an isolated area from central Sardinia.

Yes, my own case validates that. I'm half Emilian and half a mixture of La Spezia and Massa Carrara, and I almost always come out midway between the Bergamo sample and the Firenze sample. I guess I'm sort of sitting on the top of the Appennini. :) When the Piemonte sample is present, I'm closest to that.

I think that in the actual Sardinia paper they discuss the difference between the Cavalli-Sforza samples and their own, and they say the Cavalli-Sforza samples are not "quite" as isolated as their own, but again, having a grasp of the Italian "genetic landscape", he knew what he was doing.

In terms of these calculators, it's sometimes difficult to know what Italian samples the creators are using. In the Dienekes spreadsheets he helpfully tells you, so his own North Italian sample is labeled "Dodecad". The HGDP Bergamo sample is North_Italians. With other amateur bloggers I suppose they have to be asked if they don't helpfully list a sample as "Piemonte" for example.

Pax Augusta
22-12-16, 20:01
Yes, my own case validates that. I'm half Emilian and half a mixture of La Spezia and Massa Carrara, and I almost always come out midway between the Bergamo sample and the Firenze sample. I guess I'm sort of sitting on the top of the Appennini. :)

That's a nice sitting, lots of good tasting chestnuts, cheese, sausages and honey on the top of Appennini. :) I go there sometimes, I have friends who live there.


I think that in the actual Sardinia paper they discuss the difference between the Cavalli-Sforza samples and their own, and they say the Cavalli-Sforza samples are not "quite" as isolated as their own, but again, having a grasp of the Italian "genetic landscape", he knew what he was doing.

On Sardinians I've found this, it comes from an Italian book that I've yet to buy.

http://i.imgur.com/3xyS5lH.jpg


The rest of Italy

http://i.imgur.com/reYoJLF.jpg

NB, the hotspot of the Etruscan influence seems in northern Lazio rather than in southern Tuscany

http://i.imgur.com/EpSi0DL.jpg

http://i.imgur.com/8evAY0u.jpg




When the Piemonte sample is present, I'm closest to that. In terms of these calculators, it's sometimes difficult to know what Italian samples the creators are using. In the Dienekes spreadsheets he helpfully tells you, so his own North Italian sample is labeled "Dodecad". The HGDP Bergamo sample is North_Italians. With other amateur bloggers I suppose they have to be asked if they don't helpfully list a sample as "Piemonte" for example.

Isn't the Piedmont sample from Val Borbera used in some papers? I remember a paper about a community from Val Borbera that was considered an isolated population.

Angela
22-12-16, 20:59
That's a nice sitting, lots of good tasting chestnuts, cheese, sausages and honey on the top of Appennini. :) I go there sometimes, I have friends who live there.



On Sardinians I've found this, it comes from an Italian book that I've yet to buy.

http://i.imgur.com/3xyS5lH.jpg


The rest of Italy

http://i.imgur.com/reYoJLF.jpg

NB, the hotspot of the Etruscan influence seems in northern Lazio rather than in southern Tuscany

http://i.imgur.com/EpSi0DL.jpg

http://i.imgur.com/8evAY0u.jpg





Isn't the Piedmont sample from Val Borbera used in some papers? I remember a paper about a community from Val Borbera that was considered an isolated population.

I think so, but as I said these amateur bloggers aren't very clear, some of them, what samples they're using. If this is the Piemonte sample, I understand why he called it that, given that it's technically in the provincia di Alessandria, but it's really more a Ligurian sample, don't you think? Given that the boundaries are Piazenza, Alessandria, Genova and western Emilia, I think of it as the Quattro Province sample.

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

This is the study that describes the collection of the results:
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0007554

Here is what they say:
" Analysis of the large genealogy constructed starting from city and parish archives showed not only that endogamy was high in the past, but also that >90% of the participants to the study had 4 grandparents born in the valley and that 87% were connected in a unique large genealogical tree that included up to 16 generations tracing back to the 16th century."

That's exactly what Cavalli-Sforza found out about my father's villages in Emilia.

Could I have the title and author of that book? Going by those graphics, about 3/4 of my ancestry is from Ligure areas, which I had already figured out, but it would be nice to read more in depth about it. (Gaulish tribes also arrived in my father's area, however, from the migrations around 400 BC) It's nice to see one of my old theories validated as well, that Ravenna and Ferrara are probably enriched in Greek ancestry.

Is that Casentino that they propose to also harbor ancient Etruscan ancestry?

Lots of great stuffed pasta with burro and panna up there too. :)