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PCA samples from Lombard period cemetery at Collegno (6th-7th century A.D.), Italy
PCA samples from Lombard period cemetery at Szólád (6th century A.D.), Hungary
PCA with Collegno and Szólád samples
I decided to poke around with Global25 and PAST. I produced these two PCAs:
Where were you able to obtain those sub-regional Italian populations? The ones I used in the generic Global25 are not very good or informative, imo.
Also, if anyone has the coordinates for the Raveane et al 2018 paper, I think that would be very useful.
global 25 is just another amateur tool, but the first PCA based on component 1 and component 2 (PC1 and PC2) is more accurate than the second one, which is based on component 1 and component 3 and thus ends up producing less accurate results.
Here is a new one I put together with the grouping changed; it is of Southern Europe. I had downloaded the Reich Lab datasets, and checked the locations of the samples, that are in the Global25 data set. I see the Southern Samples are from Cortenza, in Calabria, two from Naples, and one from Crispiano, in Puglia. The Crispiano one is the one in the Abruzzo cluster. They're from Nick Patterson et al 2012. I assume the east and west Sicilian samples are from Syracuse, and Trapani, but I could not verify that.
I combined the Cretan cluster, with Thessaloniki, to show a more proper range of where Greeks cluster. This also shows how much Western Jews, have received from Greek DNA.
I included the top ten samples I match with on Mytrueancestry.
I don't agree with where some of these samples are landing, considering where they did on the actual papers. I would like to figure out how to produce the coordinates myself from the available datasets from the Reich lab.
Yes, the east and west Sicilian samples are usually from Syracuse and Trapani.
Instead Tuscany are 5 individuals from TSI sample based on people who have at least 3 out of 4 grandparents born in Tuscany (so not the best of accuracy. There are many Tuscans who are more northwest than TSI) and Bergamo is based on 6 individuals from Bergamo HGDP (who in total are 13).
The red label of each population shoul be located where there is the average of the population. Clearly this is on the assumption that the Global25 modern samples are truly accurate and representative.
I've updated the group to be called TSI. They are indeed from that population sample.
Here is a new one I put together with the grouping changed; it is of Southern Europe. I had downloaded the Reich Lab datasets, and checked the locations of the samples, that are in the Global25 data set. I see the Southern Samples are from Cortenza, in Calabria, two from Naples, and one from Crispiano, in Puglia. The Crispiano one is the one in the Abruzzo cluster. They're from Nick Patterson et al 2012. I assume the east and west Sicilian samples are from Syracuse, and Trapani, but I could not verify that.
I combined the Cretan cluster, with Thessaloniki, to show a more proper range of where Greeks cluster. This also shows how much Western Jews, have received from Greek DNA.
I included the top ten samples I match with on Mytrueancestry.
I don't agree with where some of these samples are landing, considering where they did on the actual papers. I would like to figure out how to produce the coordinates myself from the available datasets from the Reich lab.
This is excellent, Jovialis, especially showing the whole range of Greeks. Did you think of just seeing where "Peloponnese" and "Central Greeks would land or did the author not make those samples publicly available. Reich might have them, although he wasn't on the original paper on the genetics of the Peloponnese.
This is much more in line with what is shown in the papers in terms of other statistical type tools, and that's with using Global 25 samples which were chosen with who knows what criterion. Congratulations!
If you have some time at some point, there are academic samples which are labeled Piemonte but are really the border area between Piemonte, the Ligurian Alps etc. They might be from the Estonian Biocenter. I know MDLP got them. Also, would it be a lot of trouble to put CL36 and CL23 on the PCA? They might fit in between Bergamo and Toscana, as, of course, would some Tuscan samples. CL36, at least, comes out Northern Italian sometimes, and Tuscan sometimes. Who knows why Global 25 chose the Tuscan and Bergamo samples they chose.
my wife's first 25
I got the idea from the Lazaridis PCA that included Cretans and Thessaloniki in the grouping of "Modern Greeks". Also the paper on the Peloponnese indeed confirms the Peloponnesians do cluster next to Cretans. By putting both Crete and Thessaloniki in the same group, it stretched the range.
Thanks! Here's an updated version:
I got the idea from the Lazaridis PCA that included Cretans and Thessaloniki in the grouping of "Modern Greeks". Also the paper on the Peloponnese indeed confirms the Peloponnesians do cluster next to Cretans. By putting both Crete and Thessaloniki in the same group, it stretched the range.
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