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) identified three major Sardinia-specific 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 identified 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.

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.

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%).

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.

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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