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Thread: Corsican DNA

  1. #1
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    2 out of 2 members found this post helpful.

    Corsican DNA

    https://www.biorxiv.org/content/10.1101/722165v1

    Genome-wide analysis of Corsican population reveals a close affinity with Northern and Central Italy
    Fathers mtdna T2b17
    Grandfather mtdna T1a1e
    Sons mtdna K1a4o
    Mum paternal line R1b-S8172
    Grandmum paternal side I1d1-P109
    Wife paternal line R1a-Z282

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    wish there was more!!

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    1 out of 2 members found this post helpful.
    Quote Originally Posted by Wheal View Post
    wish there was more!!
    If you mean the whole paper, Wheal, it's there. Just always look to the upper right and click on pdf.


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    I would like to see how it compares to this paper
    https://journals.plos.org/plosone/ar...l.pone.0200641

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    0 out of 1 members found this post helpful.
    Sixteen samples isn't a lot, but they did get some new comparison samples too, and with autosomal analysis you don't need as many samples as for uniparental analysis.

    "Corsicansshow an excess of RoHs indicated by the high median values of total number andtotal length of RoHs, next to Sardinians and French Basques (Fig. 1). Thishomozygosity pattern is characteristic of isolated populations with relatively loweffective population size (Ne) and high degree of endogamy29–31."

    We suspected the similarity to Tuscans, as the Corsican language bears some similarity to Tuscan.

    "To position Corsicans in the context of their geographic neighbours we used anunsupervised clustering approach32 implemented in the program ADMIXTURE33. Atthe level of lowest cross-validation index (K=6), Corsicans and geographically relatedpopulations are composed mainly by three ancestry components - “Sardinian”,“Northern and Eastern Europe”, “Caucasus and Middle East” (dark blue, light blue,and lime green respectively; Fig. 2, Supplementary Fig. S1, S2). Corsicans are mostsimilar to North-Central Italian populations (Piedmont, Lombardy, Tuscany),displaying a slightly larger proportion of a modal component in Sardinians."

    "Analysis of average population pairwise Fst distance confirms ADMIXTURE resultsshowing shortest genetic distances between geographically close mainlandpopulations and revealing larger distances with Sardinians and French Basques(Supplementary Table S2)."

    F3 shows something different:

    "To evaluate the genetic affinity between Corsica and neighbouring populations wecarried out f3-statistics analysis. Outgroup f3 statistics measures the amount ofshared genetic drift between two populations from an outgroup34. The results showedhigh affinity of Corsicans with Sardinians and French Basques, followed, as with theADMIXTURE and FST analyses, by Northern Italians and a series of mainlandEuropean populations (Supplementary Fig. S3A). The tests of admixture based onthe f3 statistics revealed an overall complexity in the admixture history of Corsica.Out of 2,652 tests performed, 18 were statistically significant (Supplementary Fig.S3B), and most of them described Corsica as a combination of Sardinian andCaucasus/Northern European contributions. Moreover, six tests includingpopulations from North African/Arabia and one from Northern Europe werestatistically significant."

    "At a finer inspection, out of the 16 Corsican samples analysed, 12 formed apopulation specific cluster (Corsicans2) in the Southern European clade, related toNorth and Central Italian group. Three samples fell into three different clusterscomposed by North and Central Italians (NorthCentralItaly), French (French) andIberians (Iberia2), respectively (Fig. 3, Supplementary Fig. S4), possibly reflecting recent relationship with mainland populations. The remaining Corsican individualformed a separate branch, closest to Portuguese and Spaniards (Iberia1). Sardiniansand French Basques group with neighbouring populations: the former with SouthernEuropeans while the latter with Northern and Western Europeans."

    In order to explore the relationships between populations, we performed a PrincipalComponent Analysis (PCA) based on the chunkcount coancestry matrix. The firsttwo PCs explain a large proportion of the total variance (55% and 19% respectively,Fig. 3B), confirming the efficacy in summarizing the genomic information of thepainting approach. The first principal component separates populations along aNorth-South axis, placing North-East Europeans on one side (left) and NearEast/Caucasus populations to the opposite (right). The second component separatespopulations along a West-East axis, with Sardinians and French Basques being clearoutliers. Most Corsican samples group together close to Italian and Spanishpopulations; the four samples that did not group with Corsican main cluster, occupyoutlier positions also in the PCA."

    What the heck? Did anyone get to the Supplementary section? They did or didn't do the four grandparent test?

    I must say I'm not impressed.

    "we performed two different GLOBETROTTER analyses,“full” and “non-local”, as previously reported37,38 (Fig. 4, Supplementary Fig. S7 andTable S4). The “full” analysis considers all samples as possible sources, while “nonlocal” excludes Southern European clusters as donors. In both the analysis, a singleadmixture involving more than one source was identified for the main Corsicancluster. This admixture involved North and West Europe and Levant/North Africansources, and occurred between 37 and 76 generations ago, a time period spanningthe fall of the Roman Empire and the invasions by Barbarians and Saracens.In the “full” analysis, the admixture sources included Sardinians, NorthCentralItalians, Spanish and Sicilians (Supplementary Table S4), possibly suggesting geneflows from continental Europe, while the Levant/North African contribution inferred inthe “non-local” analysis was most probably passed to Corsicans hitchhiking onmainland populations. Similar admixture profiles were observed for two Sardinianclusters, with central time estimates of 59 and 44 generations ago. These resultssuggest that similar admixture episodes affected both the Mediterranean islands. The impact of North Africa and Levant is also evident in the remaining Italian and Iberiansamples, highlighting the wide impact of the event."

    Well, doing the analysis with non-Southern European sources from northern Europe was a complete waste of time. There were no north and west Europeans on Corsica at the relevant time.

    At the same time, no, any "NA or Levant" ancestry need not have "piggy-backed" with migration from the European mainland. Were they too busy to just even use google? Corsica had its own Carthaginian and Saracen past, in the latter case coming from El Andalus. Plus, how much "Levantine" and "North African" do they think Piedmont and Tuscany could have contributed to the Corsicans when they barely have any themselves, and there wasn't a "mass" migration anyway. (If I'm reading it correctly, their "Event 1 and Event 2" analysis is total bilge. )



    "In our analysis, the Corsican samples were characterised by a highancestry of European Early Neolithic (56%), similarly to Italian, Spanish and Balkanpopulations (Fig. 5B). In addition, Corsica harboured a relatively high proportionrelated to Iranian Neolithic (22%), while the contribution of Western and EasternHunter Gatherer (WHG, EHG) was smaller, about 11%. According to previousresearches, a substantial proportion of the EHG and Iranian Neolithic (related toCaucasus Hunter Gatherer, CHG) trace back to Bronze Age movements from theSteppe, however, Iranian Neolithic could have arrived to Western Mediterranean withdifferent migration38–40. This seems to be supported also for Corsica when qpAdmanalysis including Steppe_EMBA (Early Middle Bronze Age) and Iranian Neolithic(Iran_N) were considered in the same analysis evaluating the proportions (AnatoliaNeolithic: 33%, Steppe_EMBA: 19%, Iran Neolithic: 14%, Europe MiddleNeolithic/Chalcolithic: 34%). Compared to Corsicans, French and Spanish sampleswere characterised by a smaller proportion of Iranian Neolithic (13% and 15%,respectively), and a slightly higher contribution from Western Hunter Gatherers (14%and 17%).

    Big whoops. In looking at the admixture analysis I'm thinking how they and most geneticists and we amateurs, including me, spend so much time parsing the small differences between groups when in all actuality the differences are so minor. Just look at the block of Southern Europeans. If we zoomed out a bit it would just be a big mass.
    [IMG][/IMG]


    Sorry, guys, I'm just getting a bit bored with all of this, and a bit tired of reading sloppy work. Just as an example, when they say Corsicans have a similarity to the people of Piedmont, what they really mean is that they show a similarity to the people from that sample stupidly labeled Piemonte which is in fact from mountainous Liguria. The names of the villages all have Ligure in them, they speak a Ligurian dialect, and they were only recently incorporated into Piemonte. So, as makes perfect sense given for how many centuries Corsica was ruled by Genova, the Corsicans have an affinity for "Ligurians", not particularly the people of Piemonte. Genova didn't just "rule" Corsica, there was migration from Genova "to" Corsica, as in the famous case of Napoleon's mother's family.

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    1 out of 1 members found this post helpful.
    I rather agree with your above post, Angela.

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