Reconstructing Sardinian population history

A very interesting pre-pub study, dealing with Sardinian genetics in great sub-national detail but also within the wider European and Mediterranean context, became available in the last weeks. I won't probably be able to make justice to it here, so please take a look yourselves.

Charleston W.K. Chiang et al., Population history of the Sardinian people inferred from whole-genome sequencing. BioRXiv 2016. Open access pre-pub → LINK [doi:10.1101/092148]

Abstract

The population of the Mediterranean island of Sardinia has made important contributions to genome-wide association studies of traits and diseases. The history of the Sardinian population has also been the focus of much research, and in recent ancient DNA (aDNA) studies, Sardinia has provided unique insight into the peopling of Europe and the spread of agriculture. In this study, we analyze whole-genome sequences of 3,514 Sardinians to address hypotheses regarding the founding of Sardinia and its relation to the peopling of Europe, including examining fine-scale substructure, population size history, and signals of admixture. We find the population of the mountainous Gennargentu region shows elevated genetic isolation with higher levels of ancestry associated with mainland Neolithic farmers and depleted ancestry associated with more recent Bronze Age Steppe migrations on the mainland. Notably, the Gennargentu region also has elevated levels of pre-Neolithic hunter-gatherer ancestry and increased affinity to Basque populations. Further, allele sharing with pre-Neolithic and Neolithic mainland populations is larger on the X chromosome compared to the autosome, providing evidence for a sex-biased demographic history in Sardinia. These results give new insight to the demography of ancestral Sardinians and help further the understanding of sharing of disease risk alleles between Sardinia and mainland populations.

The authors call to some question the extreme simplicity of the three populations model of Lazaridis and subsequent studies. They do not flatly reject it but it seems that the lack of nuance bothers them a lot, as it does to me. This is quite clear when they find once and again Sardinian-Basque lines of relationship without going through Italian, Spaniard or French intermediaries, also when they face the issue of the largest Y-DNA haplogroups in the island, I2a1a (M26, almost exclusively a Sardinian and Pyrenean haplogroup) and R1b1a2 (M269), which are not typically associated with Neolithic farmers, suggesting that there is more to Neolithic settlement than meets the eye in the too simplistic three populations' model. They even seem to consider if Paleolithic peoples from Sardinia itself or maybe some other locations contributed heavily to what they feel is a sex-biased genetic pool.

They do confirm that Sardinians have both strong "Neolithic" (Stuttgart) and "Paleolithic" (Lochsbour) ancestry and no (negative even) "Steppe" (Yamnaya) one, although this last is truer for the most isolated sub-populations than for the more cosmopolitan ones. 

They also estimate that Sardinians have been generally isolated from the rest of Europeans for some 330 generations, what reads as approx. 9900 years, i.e. since the very early Neolithic settlement of the island. We would actually have to reduce that time span a bit but within reason, else it becomes Epipaleolithic in fact, what is most unlikely. Alternatively, as the main comparison is Northern Europe, this date could refer to the branching out of Painted-Linear (continental) and Impressed-Cardium (maritime) Neolithic cultures in the Aegean or the Balcans.