Reply With QuoteSome interesting bits:
" PCA shows a one-dimensional isolation-by-distance configuration around the Mediterranean, from North Africa through the Near East and then towards Iberia (Novembre and Stephens 2008, Henn et al. 2012, Botigue et al. 2013, Paschou et al. 2014) (Figure 4A,). The effective migration surface shows the Mediterranean Sea as having low effective migration (Figure 4B), isolating Sardinia"from neighboring mainland populations, with stronger isolation between Sardinia and North Africa than mainland Europe (Figure 4B).
I tried to explain how difficult it is to go directly from the mainland to Sardinia and even more so from North Africa to Sardinia because of the air and sea currents, but it was heavy going. Maybe women are presumed to know nothing about navigation. Now here is the proof in genetics.
"As an alternative visualization of pan-Mediterranean population structure, an analysis using the ADMIXTURE software inferred four ancestral components, with one component associated primarily with Sardinians and Southern Europeans (“red”), and remaining components corresponding to North African (“blue”), Middle East and Caucasus (“purple”), and Northern Europeans (“green”) (Figure 4C; see Figure S3 for results at other values of K). The Arzana individuals contained 100% of this red component and Sardinians from Cagliari contained 93% of this red component."
"e sharing with admixed Latino populations may reflect variants shared between Sardinian ancestors and ancestral European sources to admixed Latino populations (e.g. Iberian populations)."
"Due to its smaller long-term effective population size (Figure 5A), Sardinia is expected to have undergone accelerated rates of genetic drift. To correct for this when measuring similarity to other mainland populations, we used “shared drift” outgroup-f3 statistics (Raghavan et al. 2014), which are robust to population-specific drift. Using this metric, we find the Basque are the most similar to Sardinia, even more so than neighboring mainland Italian populations such as Tuscany and Bergamo (Figure S6A, S6B). This relationship is corroborated by identityby-descent (“IBD”) tract length sharing, where among mainland European populations, French Basque showed the highest median length of shared segments (1.525 cM) with Arzana."
We also tested the affinity between Sardinians and Basque with the D-statistics of the form D(Outgroup, Sardinia; Bergamo or Tuscan, Basque)...We find that Sardinia consistently showed increased sharing with the Basque populations compared to mainland Italians...In contrast, sharing with other Spanish samples in our dataset was generally weaker and not significant ( |Z| < 3.5; Figure S6C), suggesting the shared drift with the Basque is not mediated through Spanish ancestry."
This might be an indication that there were once French Basque like populations throughout southern France which then moved into Sardinia. While it's true, as I said, that it's difficult to reach Sardinia from the mainland, the route from southern France/northeast Spain to Sardinia isn't too bad. The other "relatively" easy trip is by sea from Greece, southern Italy, Sicily etc.
They do a much better job than Hellenthal at explaining any "recent" admixture in Sardinia. There is no indication of it in mainland, central Sardinia. One test failed to disclose any even in areas like Cagliari, the capitol, but one did find some.
"h previous reports (Moorjani et al. 2011, Loh et al. 2013, Hellenthal et al. 2014). For example, Cagliari individuals demonstrated ~7% of a non-Sardinian (“purple”) component that is found in substantial fraction among extant individuals from Southern Europe, Middle East, Caucasus, and North Africa. To assess this in detail we used the f3-test for admixture (Patterson et al. 2012) and found none of the Sardinian populations showed any evidence of admixture. In contrast, mainland Europeans, particularly Southern Europeans, show evidence of admixture from Near East and sub-Saharan Africa (Figure S8). Because f3-based tests for admixture may lose power when applied to populations that have experienced extensive drift post-admixture (Patterson et al. 2012), we also used a complementary LD-based approach (ALDER, Loh et al. 2013) to test each Sardinian population for admixture. Using this approach, a number of Sardinian populations, particularly those outside of Ogliastra, are inferred to be admixed (Table 1, Table S4). The inferred source populations are typically a mainland Eurasian population and a sub-Saharan African population. The admixture proportions range from 0.9% to 4% of sub-Saharan ancestry by the f4 ratio test (Patterson et al. 2012) (Table 1, Table S4) with estimated admixture dates of approximately 59-109 generations."
"found the best proxy for African admixture is sub-Saharan African populations, rather than Mediterranean North African populations, and we inferred the date of admixture as approximately 1,800-3,000 years ago (assuming 30 years per generation).
I differ with them in the following to the extent that I don't think that there was large scale migration from the Near East with the Arab invasions, although there was some.
"lack of a strong signal of North African autosomal admixture may be due to inadequate coverage of modern North African diversity in our reference sample. Alternatively, it may be due to a poor representation of ancestral North Africans. Present-day North African ancestry reflects large-scale recent gene flow during the Arab expansion (~1,400 years ago (Henn et al. 2012)). The sub-Saharan African admixture observed in the non-Ogliastra samples could be mediated through an early influx of migrants from North Africa prior to the Arab expansion, for example during the eras of trade relations and occupations from the Phoenicians, Carthaginians, and Romans (~700 B.C.- ~200 B.C.;"
"both ancient Neolithic farmer ancestry and pre-Neolithic ancestry are enriched in the Gennargentu-region. First, we find that shared drift with Neolithic farmers and with pre-Neolithic hunter-gatherers is significantly correlated with the proportion of “Gennargentu-region” ancestral component estimated from ADMIXTURE analysis, while shared drift with Steppe pastoralists has a weak negative correlation with Gennargentu-region ancestry (Figure 6B). Second, using supervised estimation of ancestry proportion based on aDNA (Haak et al. 2015), we estimate higher levels of Neolithic and preNeolithic ancestries in the Gennargentu region and higher levels of Steppe Pastoralist ancestry outside the region (Figure S10)"
"Intriguingly, on average, we find a higher proportion of the Gennargentu-region ancestry (“red” component in Figure S11) on the X-chromosome (37%) than on the autosome (30%, P < 1e-6 by permutation). As the Gennargentu-region ancestry is correlated with more ancient, Neolithic or pre-Neolithic ancestries rather than Bronze Age ancestries (Figure 6B), this finding suggests sex-biased processes in which more females than males carried the non-Steppe ancestries."
"These results demonstrate that sex-biased process occurred in the founding of Sardinia, which is above and beyond any putative sex-biased processes on the mainland."
I have some skepticism about this:
"Our analysis of crosscoalescent rates suggest the population lineage ancestral to modern-day Sardinia was effectively isolated from the mainland European populations approximately 330 generations ago. This estimate should be treated with caution, but corresponds to approximately 9,900 years ago assuming a generation time of 30 years and mutation rate of 1.25x10-8 per basepair per generation."
Here they address the point I raised about the uncertainty as to where the WHG ancestry was added:
. That pre-Neolithic hunter-gatherer and Neolithic farmer ancestry are enriched in this region of isolation suggests that the early populations of Sardinia were an admixture of the two ancestries, rather than the pre-Neolithic ancestry arriving via later migrations from the mainland. However, it remains to be seen whether this admixture principally occurred on the island or on the mainland prior to a Neolithic era influx to the island."
"The high frequency of particular Y-chromosome haplogroups (particularly I2a1a2 and R1b1a2) that are not commonly affiliated with Neolithic ancestry is one challenge to a model in which Sardinian principally has Neolithic ancestry."
I don't see the problem with the above. We already know of I2a1a2 samples from the mainland which are typically European farmer. They apparently represent absorbed male hunter-gatherer lines.
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Originally Posted by srdceleva
