Ancient Sardinia hints at Mesolithic spread of R1b-V88, and Western EEF-related expansion of Vasconic

New preprint Population history from the Neolithic to present on the Mediterranean island of Sardinia: An ancient DNA perspective, by Marcus et al. bioRxiv (2019)

Interesting excerpts (emphasis mine, edited for clarity):

On the high frequency of R1b-V88

Our genome-wide data allowed us to assign Y haplogroups for 25 ancient Sardinian individuals. More than half of them consist of R1b-V88 (n=10) or I2-M223 (n=7).

Francalacci et al. (2013) identi fied three major Sardinia-specifi c founder clades based on present-day variation within the haplogroups I2-M26, G2-L91 and R1b-V88, and here we found each of those broader haplogroups in at least one ancient Sardinian individual. Two major present-day Sardinian haplogroups, R1b-M269 and E-M215, are absent.

Compared to other Neolithic and present-day European populations, the number of identi fied R1b-V88 carriers is relatively high.

(…)ancient Sardinian mtDNA haplotypes belong almost exclusively to macro-haplogroups HV (n = 16), JT (n = 17) and U (n = 9), a composition broadly similar to other European Neolithic populations.

r1b-v88-europe
Geographic and temporal distribution of R1b-V88 Y-haplotypes in ancient European samples. We plot the geographic position of all ancient samples inferred to carry R1b-V88 equivalent markers. Dates are given as years BCE (means of calibrated 2s radio-carbon dates). Multiple V88 individuals with similar geographic positions are vertically stacked. We additionally color-code the status of the R1b-V88 subclade R1b-V2197, which is found in most present-day African R1b-V88 carriers.

On the origin of a Vasconic-like Paleosardo with the Western EEF

(…) the Neolithic (and also later) ancient Sardinian individuals sit between early Neolithic Iberian and later Copper Age Iberian populations, roughly on an axis that differentiates WHG and EEF populations and embedded in a cluster that additionally includes Neolithic British individuals. This result is also evident in terms of absolute genetic differentiation, with low pairwise FST ~ 0.005 +- 0.002 between Neolithic Sardinian individuals and Neolithic western mainland European populations. Pairwise outgroup-f3 analysis shows a very similar pattern, with the highest values of f3 (i.e. most shared drift) being with Neolithic and Copper Age Iberia, gradually dropping off for temporally and geographically distant populations.

In explicit admixture models (using qpAdm, see Methods) the southern French Neolithic individuals (France-N) are the most consistent with being a single source for Neolithic Sardinia (p ~ 0:074 to reject the model of one population being the direct source of the other); followed by other populations associated with the western Mediterranean Neolithic Cardial Ware expansion.

sardinians-ancient-eef
Principal Components Analysis based on the Human Origins dataset. A: Projection of ancient individuals’ genotypes onto principal component axes de fined by modern Western Eurasians (gray labels).

Pervasive Western Hunter-Gatherer ancestry in Iberian/French/Sardinian population

Similar to western European Neolithic and central European Late Neolithic populations, ancient Sardinian individuals are shifted towards WHG individuals in the top two PCs relative to early Neolithic Anatolians Admixture analysis using qpAdm infers that ancient Sardinian individuals harbour HG ancestry (~ 17%) that is higher than early Neolithic mainland populations (including Iberia, ~ 8%), but lower than Copper Age Iberians (~ 25%) and about the same as Southern French Middle-Neolithic individuals (~ 21%).

sardinia-modern-ancient-nuragic-pca
Principal Components Analysis based on the Human Origins dataset. B: Zoom into the region most relevant for Sardinian individuals.

Continuity from Sardinia Neolithic through the Nuragic

We found several lines of evidence supporting genetic continuity from the Sardinian Neolithic into the Bronze Age and Nuragic times. Importantly, we observed low genetic differentiation between ancient Sardinian individuals from various time periods.

A qpAdm analysis, which is based on simultaneously testing f-statistics with a number of outgroups and adjusts for correlations, cannot reject a model of Neolithic Sardinian individuals being a direct predecessor of Nuragic Sardinian individuals (…) Our qpAdm analysis further shows that the WHG ancestry proportion, in a model of admixture with Neolithic Anatolia, remains stable at ~17% throughout three ancient time-periods.

sardinians-modern-ancient-pca-admixture
Present-day genetic structure in Sardinia reanalyzed with aDNA. A: Scatter plot of the rst two principal components trained on 1577 present-day individuals with grand-parental ancestry from Sardinia. Each individual is labeled with a location if at least 3 of the 4 grandparents were born in the same geographical location (\small” three letter abbreviations); otherwise with \x” or if grand-parental ancestry is missing with \?”. We calculated median PC values for each Sardinian province (large abbreviations). We also projected each ancient Sardinian individual on to the top two PCs (gray points). B/C: We plot f-statistics that test for admixture of modern Sardinian individuals (grouped into provinces) when using Nuragic Sardinian individuals as one source population. Uncertainty ranges depict one standard error (calculated from block bootstrap). Karitiana are used in the f-statistic calculation as a proxy for ANE/Steppe ancestry (Patterson et al., 2012).

Steppe influx in Modern Sardinians

While contemporary Sardinian individuals show the highest affinity towards EEF-associated populations among all of the modern populations, they also display membership with other clusters (Fig. 5). In contrast to ancient Sardinian individuals, present-day Sardinian individuals carry a modest “Steppe-like” ancestry component (but generally less than continental present-day European populations), and an appreciable broadly “eastern Mediterranean” ancestry component (also inferred at a high fraction in other present-day Mediterranean populations, such as Sicily and Greece).

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17 thoughts on “Ancient Sardinia hints at Mesolithic spread of R1b-V88, and Western EEF-related expansion of Vasconic

  1. These have been a great set of papers. My initial impression (subject to further analysis) is that there is little if any support for a Nurago-Vasconic hypothesis, as there is a complete disjunction of male uniparental markers (Mediterranean Chalcolithic -derived G2a, I2a1a, R1b-V88 vs Iberian Beaker-derived R1b-DF 27), different autosomic features, etc. They seem to be results of different phenomena.

    1. There seems to be a clear genetic link through a kind of “western EEF” though, which includes Iberia, Southern France, and Sardinia, as seen in expanding Iberians in the MBA-LBA into the Balearic Islands and their link to Sardinians. Whether that link is quite early during the Cardial expansion, or maybe mediated later by the Megalithic or even Proto-Beaker expansions is still unclear.

      Even though I am a fan of following Y-DNA, I am also a fan of analyzing why certain Y-DNA expansions are not followed by their ancestral language expansions:

      – Sardinia looks, in a sense, like the Chalcolithic and Bronze Age Aegean – in terms of genetic impact of Anatolian and Proto-Greek migrations – , in this case possibly because of its isolation from the mainland and considerable size (also in population?). The survival and expansion of R1b-V88 (which the paper attributes to the Neolithic, but which is more likely linked to Mesolithic expansions) is evidence of this.

      – Regarding Y-DNA expansions of R1b-P312 from SW France (Vasconic) and SE Spain (Iberian), different R1b-P312 lineages became integrated at some point in these communities derived from Chalcolithic France and Iberia, respectively, so their expansion mark the expansion of non-Indo-European languages, and ancestry becomes then a nice tool for ascertaining from where exactly do certain communities expand.

      Anyway, the link should be done linguistically, and the Vasconic-like Paleosardo substrate hypothesis was never too strong, if only because of our ignorance of stages previous to Proto-Basque (or even of Proto-Basque itself). I still favour it, though, seeing how some “Vasconic-like” borrowings also appear in North-West Indo-European substrate, which means EEF up to Hungary could have signalled this ancestral Vasconic-Iberian language expanded with the Neolithic.

      And I certainly favour it over any link with Caucasian languages, which is based mainly on ergativity, a trait that cannot even be reconstructed for Proto-Basque…

    2. There seems to be a clear genetic link through a kind of “western EEF” though, which includes Iberia, Southern France, and Sardinia, as seen in expanding Iberians in the MBA-LBA into the Balearic Islands and their link to Sardinians. Whether that link is quite early during the Cardial expansion, or maybe mediated later by the Megalithic or even Proto-Beaker expansions is still unclear.

      Even though I am a fan of following Y-DNA, I am also a fan of analyzing why certain Y-DNA expansions are not followed by their ancestral language expansions:

      – Sardinia looks, in a sense, like the Chalcolithic and Bronze Age Aegean – in terms of genetic impact of Anatolian and Proto-Greek migrations – , in this case possibly because of its isolation from the mainland and considerable size (also in population?). The survival and expansion of R1b-V88 (which the paper attributes to the Neolithic, but which is more likely linked to Mesolithic expansions) is evidence of this.

      – Regarding Y-DNA expansions of R1b-P312 from SW France (Vasconic) and SE Spain (Iberian), different R1b-P312 lineages became integrated at some point in these communities derived from Chalcolithic France and Iberia, respectively, so their expansion mark the expansion of non-Indo-European languages, and ancestry becomes then a nice tool for ascertaining from where exactly do certain communities expand.

      Anyway, the link should be done linguistically, and the Vasconic-like Paleosardo substrate hypothesis was never too strong, if only because of our ignorance of stages previous to Proto-Basque (or even of Proto-Basque itself). I still favour it, though, seeing how some “Vasconic-like” borrowings also appear in North-West Indo-European substrate, which means EEF up to Hungary could have signalled this ancestral Vasconic-Iberian language expanded with the Neolithic.

      And I certainly favour it over any link with Caucasian languages, which is based mainly on ergativity, a trait that cannot even be reconstructed for Proto-Basque…

    3. There seems to be a clear genetic link through a kind of “western EEF” though, which includes Iberia, Southern France, and Sardinia, as seen in expanding Iberians in the MBA-LBA into the Balearic Islands and their link to Sardinians. Whether that link is quite early during the Cardial expansion, or maybe mediated later by the Megalithic or even Proto-Beaker expansions is still unclear.

      Even though I am a fan of following Y-DNA, I am also a fan of analyzing why certain Y-DNA expansions are not followed by their ancestral language expansions:

      – Sardinia looks, in a sense, like the Chalcolithic and Bronze Age Aegean – in terms of genetic impact of Anatolian and Proto-Greek migrations – , in this case possibly because of its isolation from the mainland and considerable size (also in population?). The survival and expansion of R1b-V88 (which the paper attributes to the Neolithic, but which is more likely linked to Mesolithic expansions) is evidence of this.

      – Regarding Y-DNA expansions of R1b-P312 from SW France (Vasconic) and SE Spain (Iberian), different R1b-P312 lineages became integrated at some point in these communities derived from Chalcolithic France and Iberia, respectively, so their expansion mark the expansion of non-Indo-European languages, and ancestry becomes then a nice tool for ascertaining from where exactly do certain communities expand.

      Anyway, the link should be done linguistically, and the Vasconic-like Paleosardo substrate hypothesis was never too strong, if only because of our ignorance of stages previous to Proto-Basque (or even of Proto-Basque itself). I still favour it, though, seeing how some “Vasconic-like” borrowings also appear in North-West Indo-European substrate, which means EEF up to Hungary could have signalled this ancestral Vasconic-Iberian language expanded with the Neolithic.

      And I certainly favour it over any link with Caucasian languages, which is based mainly on ergativity, a trait that cannot even be reconstructed for Proto-Basque…

      1. Carlos,
        I don’t have a strong opinion on the linguistic issue, perhaps no definitive link either way at present.

        Genetically, it seems the link refers to their common Epicardial origin and ongoing contacts during the Copper Age across the Mediterranean. Theoretically, these groups could have spoken a similar language, and continued on, but contact would been sporadic when compared to the ML Bronze Age situaion. Also, the ‘western EEF’, if such existed, was diverse within SW Europe, with Iberia acquiring central European admixture prior the Bell Beaker period, c. 45/4000 – 3000 BC. If there was a Copper Age migration from a group in Iberia CA to Sardinia, we should expect some hg I2a2 to show up in Sardinians (given that it was about 70% of Y-hgs in non-Atlantic Iberia), but this does not seem to have shown up in aDNA or modern Sardinians. It suggests to me that there was an earlier common Neolithic background followed by more differential processes during the B.A.

      2. Carlos,
        I don’t have a strong opinion on the linguistic issue, perhaps no definitive link either way at present.

        Genetically, it seems the link refers to their common Epicardial origin and ongoing contacts during the Copper Age across the Mediterranean. Theoretically, these groups could have spoken a similar language, and continued on, but contact would been sporadic when compared to the ML Bronze Age situaion. Also, the ‘western EEF’, if such existed, was diverse within SW Europe, with Iberia acquiring central European admixture prior the Bell Beaker period, c. 45/4000 – 3000 BC. If there was a Copper Age migration from a group in Iberia CA to Sardinia, we should expect some hg I2a2 to show up in Sardinians (given that it was about 70% of Y-hgs in non-Atlantic Iberia), but this does not seem to have shown up in aDNA or modern Sardinians. It suggests to me that there was an earlier common Neolithic background followed by more differential processes during the B.A.

      3. Carlos,
        I don’t have a strong opinion on the linguistic issue, perhaps no definitive link either way at present.

        Genetically, it seems the link refers to their common Epicardial origin and ongoing contacts during the Copper Age across the Mediterranean. Theoretically, these groups could have spoken a similar language, and continued on, but contact would been sporadic when compared to the ML Bronze Age situaion. Also, the ‘western EEF’, if such existed, was diverse within SW Europe, with Iberia acquiring central European admixture prior the Bell Beaker period, c. 45/4000 – 3000 BC. If there was a Copper Age migration from a group in Iberia CA to Sardinia, we should expect some hg I2a2 to show up in Sardinians (given that it was about 70% of Y-hgs in non-Atlantic Iberia), but this does not seem to have shown up in aDNA or modern Sardinians. It suggests to me that there was an earlier common Neolithic background followed by more differential processes during the B.A.

        1. Agreed, the link seems a priori (based on Y-DNA) to be ancient rather than recent, and what is found in the MBA expanding from Iberia into the Balearic Islands (similar to Sardinian ancestry) may be this ancient Early Neolithic connection.

          By “western EEF” I meant the EEF wave associated with the Cardial expansion, where it seems that varied WHG (mainly I2) lineages became associated with the spread of the Neolithic through the Mediterranean (originally apparently of G2, E and J?), at some point. It would be different from the “northern (or central European) EEF” expanding through Hungary into the LBK, visible in the formed PCA clusters, too.

          However, I guess the Megalithic expansion, if originally from north-eastern France, hence a mix with the “northern EEF” wave (based on the little we know in genetics), may be at the same time 1) a confounding factor in western European LN and Chalcolithic movements, but also 2) a very specific ancestral sign to look for, to distinguish EN (Cardial) movements from more recent LN or Chalcolithic ones in western Europe and Sardinia…

        2. Agreed, the link seems a priori (based on Y-DNA) to be ancient rather than recent, and what is found in the MBA expanding from Iberia into the Balearic Islands (similar to Sardinian ancestry) may be this ancient Early Neolithic connection.

          By “western EEF” I meant the EEF wave associated with the Cardial expansion, where it seems that varied WHG (mainly I2) lineages became associated with the spread of the Neolithic through the Mediterranean (originally apparently of G2, E and J?), at some point. It would be different from the “northern (or central European) EEF” expanding through Hungary into the LBK, visible in the formed PCA clusters, too.

          However, I guess the Megalithic expansion, if originally from north-eastern France, hence a mix with the “northern EEF” wave (based on the little we know in genetics), may be at the same time 1) a confounding factor in western European LN and Chalcolithic movements, but also 2) a very specific ancestral sign to look for, to distinguish EN (Cardial) movements from more recent LN or Chalcolithic ones in western Europe and Sardinia…

        3. Agreed, the link seems a priori (based on Y-DNA) to be ancient rather than recent, and what is found in the MBA expanding from Iberia into the Balearic Islands (similar to Sardinian ancestry) may be this ancient Early Neolithic connection.

          By “western EEF” I meant the EEF wave associated with the Cardial expansion, where it seems that varied WHG (mainly I2) lineages became associated with the spread of the Neolithic through the Mediterranean (originally apparently of G2, E and J?), at some point. It would be different from the “northern (or central European) EEF” expanding through Hungary into the LBK, visible in the formed PCA clusters, too.

          However, I guess the Megalithic expansion, if originally from north-eastern France, hence a mix with the “northern EEF” wave (based on the little we know in genetics), may be at the same time 1) a confounding factor in western European LN and Chalcolithic movements, but also 2) a very specific ancestral sign to look for, to distinguish EN (Cardial) movements from more recent LN or Chalcolithic ones in western Europe and Sardinia…

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