Population history from the Neolithic to present on the Mediterranean island of Sardi

Cato

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Recent ancient DNA studies of western Eurasia have revealed a dynamic history of admixture, with evidence for major migrations during the Neolithic and Bronze Age. The population of the Mediterranean island of Sardinia has been notable in these studies -- Neolithic individuals from mainland Europe cluster more closely with Sardinian individuals than with all other present-day Europeans. The current model to explain this result is that Sardinia received an initial influx of Neolithic ancestry and then remained relatively isolated from expansions in the later Neolithic and Bronze Age that took place in continental Europe. To test this model, we generated genome-wide capture data (approximately 1.2 million variants) for 43 ancient Sardinian individuals spanning the Neolithic through the Bronze Age, including individuals from Sardinia's Nuragic culture, which is known for the construction of numerous large stone towers throughout the island. We analyze these new samples in the context of previously generated genome-wide ancient DNA data from 972 ancient individuals across western Eurasia and whole-genome sequence data from approximately 1,500 modern individuals from Sardinia. The ancient Sardinian individuals show a strong affinity to western Mediterranean Neolithic populations and we infer a high degree of genetic continuity on the island from the Neolithic (around fifth millennium BCE) through the Nuragic period (second millennium BCE). In particular, during the Bronze Age in Sardinia, we do not find significant levels of the "Steppe" ancestry that was spreading in many other parts of Europe at that time. We also characterize subsequent genetic influx between the Nuragic period and the present. We detect novel, modest signals of admixture between 1,000 BCE and present-day, from ancestry sources in the eastern and northern Mediterranean. Within Sardinia, we confirm that populations from the more geographically isolated mountainous provinces have experienced elevated levels of genetic drift and that northern and southwestern regions of the island received more gene flow from outside Sardinia. Overall, our genetic analysis sheds new light on the origin of Neolithic settlement on Sardinia, reinforces models of genetic continuity on the island, and provides enhanced power to detect post-Bronze-Age gene flow. Together, these findings offer a refined demographic model for future medical genetic studies in Sardinia.
https://www.biorxiv.org/content/10.1101/583104v1

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modern Sardinians have really a lot of Roman/Italian admixture ("Northern Mediterranean"), it's a surprise for me

In any case very few steppe admixture circa 1-3% began to appear in the EBA (page 11) as suggested by archaeology (Bell Beaker, Polada-like Bonnanaro culture)

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There's a Punic sample from Tharros coming from a new study that seems to be an indigenous Sardinian:


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http://amsdottorato.unibo.it/8577/?...x-0QtbBpZwHqMcxLRIjOj4D9tVz-9hLRuabLyM6i8SN98
 
Percentage of Nuragic, Northern and Eastern admixtureScreenshot_20190322-093908_Adobe Acrobat.jpg

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what i find strange is the almost total lack of steppe in the EBA and Nuragic samples..even Sicilian Beaker have it! Maybe Beakers that reached Sardinia were heavily admixed with EEF?

Apparently Lazio was still EEF in the EBA too

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Thanks. I'll read it with interest. I see it's Haak and Krause again.

I want to compare their analysis of Nuragic Sardinians with that of the Reich group.

No Iron Age sample or Late Antiquity samples as with the Reich paper?
 
First off, it's a much better organized and written paper than the one from the Reich Lab by Fernandes. Second, it pays much better attention to the details of the substructure in Sardinia.

It's true that they don't have an Iron Age sample or four Late Antiquity samples, like the Reich Lab has, but I think the Reich Lab may be inferring too much from those samples in terms of the effect on modern Sardinian populations. I'm thinking particularly of the fact that this paper finds more "Levantine" in the southwest where we find evidence of Phoenician settlement, and more "northern" ancestry including Tuscan ancestry, in Olbia in the northeast and the large city of Sassari, while there is the least change in Ogliastra.
 
CA is only G2a2 and R1b-V88, no I2
EBA has arrival I2a-M26 and I2a-L161, probably from Iberian origin (Els Trocs)
J2b2a1-L283 is Nuragic, probably eastern origin
 
First off, it's a much better organized and written paper than the one from the Reich Lab by Fernandes. Second, it pays much better attention to the details of the substructure in Sardinia.

It's true that they don't have an Iron Age sample or four Late Antiquity samples, like the Reich Lab has, but I think the Reich Lab may be inferring too much from those samples in terms of the effect on modern Sardinian populations. I'm thinking particularly of the fact that this paper finds more "Levantine" in the southwest where we find evidence of Phoenician settlement, and more "northern" ancestry including Tuscan ancestry, in Olbia in the northeast and the large city of Sassari, while there is the least change in Ogliastra.

Reich is about western Med
this study zooms in on Sardegna only
 
I-M26 could be even Northern Italian given that EBA Sardinian material culture is similar to Polada (Remedello 3/3 I-M26, last one is about 2000 BC if i'm not wrong)

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Reich is about western Med
this study zooms in on Sardegna only

Yes, I'm aware, but they're saying, in effect, all Sardinians, including the ones of Ogliastra, are the same, with the same kind of admixture, and that doesn't seem to be the case.
 
The R1b-V88 in 10/25 samples is really surprising (also 2 in the Reich paper in seems), basically doubles the number of R1b-V88 we have for whole ancient Europe. At present-day V88 is found in Central Africans and some Sardinians, nowhere else in Europe.

They reanalyzed R1b-V88 - look at Supp. Mat. 4., map with ages of all R1b-V88 found throughout Europe. Seems to trace back to Mesolithic Balkans or East, and then got associated with spread of Cardial Ware (Iberian Neolithic Els Trocs has it as well) That will provide some fuel for some people on here (green Sahara, cough).
 
Good catch, Angela. Reich's present-day Sardinian samples seem to be from Ogliastra, which is not completely representative.
 
Based on the author attribution, the aDNA work is mostly from Posth/Krause; and the analysis and writing was mostly done by the Novembre lab. Well, that explains the interesting PCA.
 
This paper's PCA:
nFkLevE.png
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It doesn't seem to me the Sardinians moved very much from the Neolithic/Nuragic to the present day, in contrast to what the Reich paper seemed to be saying.

I'd have to go back over the paper again, but Reich seems to be looking at samples from all over Sardinia, including the Ogliastra samples, and saying the Ogliastra samples show as much admixture as the coastal ones, while Krause seems to be implying the Ogliastra samples might indeed show less, as well as being highly drifted.

Oh, and the "Punic" Ibiza sample is still pretty damn close to the Mycenaeans.
 
and that's the zoom in of the full PCA. The roughly 50-70 % Nuragic ancestry for present-day Sardinians (in both papers) seem very plausible.

There was obviously some gene flow and with some interesting geographical patterns. But despite the anicient IA and Antiquity coastal individuals from Reich being all over the place, the overall effects were modest. I have a feeling that some of the phrasing in the Reich paper won't make it through review.
 
and that's the zoom in of the full PCA. The roughly 50-70 % Nuragic ancestry for present-day Sardinians (in both papers) seem very plausible.

There was obviously some gene flow and with some interesting geographical patterns. But despite the anicient IA and Antiquity coastal individuals from Reich being all over the place, the overall effects were modest. I have a feeling that some of the phrasing in the Reich paper won't make it through review.

That's exactly my feeling. The statements were not nuanced enough and gave the wrong impression.

Some of these newer fellows in that lab have to be supervised more, imho.

Plus, if some of these samples are sub-standard, they shouldn't be drawing such large conclusions from them.

It doesn't inspire confidence when samples landing on Mycenaeans are said to have substantial "Morocco Late Neolithic." Nor does it help that they didn't explain the make up of those samples and that it is unknown how much Carthaginians or "Saracens" of the early Medieval period might or might not resemble them.

Despite fewer ancient samples, I'll stick with the Krause paper on this topic.

The Reich Lab had better get used to samples from all over the ancient world showing up far from "home" as they analyze the period from the first millennium B.C. It doesn't mean there were tens of thousands or more of these people and they massively changed the genome. Such judgment has to be exercised.
 
Just checked out the Supp. of Fernandes et al. Four of the Late Antiquity samples are from a cave that can be only reached by sea, without any archeological context (reads like they thought it's a potential Neolithic/Nuragic site, but the Radiocarbon dates showed they were younger). I am not a local nor archeologist, but sounds like one should be a bit careful with such sites without context, or at least point it out.

Certainly agree with you, the 1st millennium BCE with Punic/Roman Mediterranean times with big civilization and some pretty well-traveled people will likely start to show outliers (see Olalde2019, and this here) and one has to start to be very careful with single samples.


I believe both papers have interesting data. the Marcus et al paper actually has more ancient Sardinians, 43 compared to the 13 of Fernandes et al (counting working ones), and also many pre-Nuragic individual, including 4 Late Neolithic and Copper Age (which is really interesting to see where the Neolithic in Sardinia came from - an old debate)

Fernandes et al has Sicilly and Balearic islands going for it, which is really nice context.
 
Just checked out the Supp. of Fernandes et al. Four of the Late Antiquity samples are from a cave that can be only reached by sea, without any archeological context (reads like they thought it's a potential Neolithic/Nuragic site, but the Radiocarbon dates showed they were younger). I am not a local nor archeologist, but sounds like one should be a bit careful with such sites without context, or at least point it out.

Certainly agree with you, the 1st millennium BCE with Punic/Roman Mediterranean times with big civilization and some pretty well-traveled people will likely start to show outliers (see Olalde2019, and this here) and one has to start to be very careful with single samples.


I believe both papers have interesting data. the Marcus et al paper actually has more ancient Sardinians, 43 compared to the 13 of Fernandes et al (counting working ones), and also many pre-Nuragic individual, including 4 Late Neolithic and Copper Age (which is really interesting to see where the Neolithic in Sardinia came from - an old debate)

Fernandes et al has Sicilly and Balearic islands going for it, which is really nice context.

I agree that Fernandes covers more "ground", so to speak, so it isn't going to be as detailed about Sardinian genetic history as this paper, but I do think that they made some errors of judgment. As you have pointed out, there is no archaeological context for those four Late Antiquity samples. They land on Mycenaeans fwiw. I don't know how many snps they have either.

In terms of Sardinian samples I also think that Fernandes made an error in only using the HGDP samples for the "Ogliastra" group. Those are the samples that Cavalli-Sforza chose and they are not all from Ogliastra, although many of them are. The Marcus paper we are discussing here used many, many modern Sardinian samples, and grouped together a group specifically from Ogliastra.

Although different analyses showed slightly different things, this is their conclusion: "Together, these results319 suggest high levels of drift specific to Ogliastra (likely also driving the first two PCs of present-day320 Sardinian variation), but simultaneously also less admixture than other Sardinian provinces."

For "Levantine" (as a stand in for Punic admixture) they show, in a three way mix, about 16% for southwestern Sardinia, and less in the modern samples from the rest of the island. I wonder if the settlements in Sardinia remained basically "Levantine", in contrast to those in Spain which had a "Carthaginian" identity, and thus contained some "North African". Certainly the "Saracens" would have been mostly "North African", although I don't know if a Moroccan LN sample is the best one to use to measure it.

That was always my contention about "Phoenician" admixture on the island, i.e. that it would show up to some degree in the SW and less in other areas, given that the Phoenicians were not "colonizers", like the Greeks. Sardinia has been a land "apart" to some degree, the terrain lends itself to separation of groups, and so I always doubted that there was widespread admixture even in Sardinia itself. Olbia is a prime example, as is indeed the entire Northern sliver, which is more shifted to northern Italy, and speaks a different language from those of the rest of Sardinia.

Sardinia_Language_Map.png
 
So, the iron age sample from the study about the Western Mediterranean islands comes from a town called Usellus in the Campidano region. In Roman times it apparently was a Roman colony as a bronze tablet found there suggests, the colony was probably founded around the second century bc, so isn't it possible for that sample to be a Roman colonist? As for the late antiquity samples, they all come from one site, a cave that can only be reached by the sea near the Sardinian capital of Cagliari (Cava dei Colombi), a strange place to bury the dead.
 

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