Angela
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This is one of the papers I've been waiting for, and it's behind a pay wall. Oh well...
The Italian genome reflects the history of Europe and the Mediterranean basin
http://www.nature.com/ejhg/journal/vaop/ncurrent/suppinfo/ejhg2015233s1.html?url=/ejhg/journal/vaop/ncurrent/abs/ejhg2015233a.html
"Abstract
Recent scientific literature has highlighted the relevance of population genetic studies both for disease association mapping in admixed populations and for understanding the history of human migrations. Deeper insight into the history of the Italian population is critical for understanding the peopling of Europe. Because of its crucial position at the centre of the Mediterranean basin, the Italian peninsula has experienced a complex history of colonization and migration whose genetic signatures are still present in contemporary Italians. In this study, we investigated genomic variation in the Italian population using 2.5 million single-nucleotide polymorphisms in a sample of more than 300 unrelated Italian subjects with well-defined geographical origins. We combined several analytical approaches to interpret genome-wide data on 1272 individuals from European, Middle Eastern, and North African populations. We detected three major ancestral components contributing different proportions across the Italian peninsula, and signatures of continuous gene flow within Italy, which have produced remarkable genetic variability among contemporary Italians. In addition, we have extracted novel details about the Italian population’s ancestry, identifying the genetic signatures of major historical events in Europe and the Mediterranean basin from the Neolithic (e.g., peopling of Sardinia) to recent times (e.g., ‘barbarian invasion’ of Northern and Central Italy). These results are valuable for further genetic, epidemiological and forensic studies in Italy and in Europe."
I really love no information abstracts, don't you?
This is the link to the Supplementary Info:
http://www.nature.com/ejhg/journal/...g/journal/vaop/ncurrent/abs/ejhg2015233a.html
I've gone through it all and I have some thoughts, but it's too late to get into it now. I'll just say that although it's better than the Busby effort, some of the choices are still obscure to me, and at least in the supplement there is no clarity as to the direction of the gene flow. Maybe if I can get my hands on the actual paper it will seem clearer, but I also get the feeling, as I did with the Busby paper, that I'm back to a time five years or more in the past before Lazaridis et al or Haak et al and Allentoft et al.
To get started, nothing really new on the PCA front except that Armenians are so removed from other Near Easterners. Turks as well to a certain extent. :
There's also a graphic on Italian variation. The general cline is as expected, except that Calabrians (Reggio Calabria) are south of some of the Sicilians. That may have to do with the samples chosen for Sicily, which are Trapani and Ragusa. I doubt that there'd be much difference between Reggio and, say, Messina, but some Sicilian posters might know better. Also, there are some samples floating out of the expected cline in north and central Italy. This may have to do with the fact that there has been a certain amount of intermarriage across provincial lines in northern and central Italy starting around the end of the 19th century. I can't see anything in the supplement as to their standards for sample inclusion. Not that it would make much difference, but I don't know why they would have chosen Ferrara for Emilia Romagna.
The Italian genome reflects the history of Europe and the Mediterranean basin
http://www.nature.com/ejhg/journal/vaop/ncurrent/suppinfo/ejhg2015233s1.html?url=/ejhg/journal/vaop/ncurrent/abs/ejhg2015233a.html
"Abstract
Recent scientific literature has highlighted the relevance of population genetic studies both for disease association mapping in admixed populations and for understanding the history of human migrations. Deeper insight into the history of the Italian population is critical for understanding the peopling of Europe. Because of its crucial position at the centre of the Mediterranean basin, the Italian peninsula has experienced a complex history of colonization and migration whose genetic signatures are still present in contemporary Italians. In this study, we investigated genomic variation in the Italian population using 2.5 million single-nucleotide polymorphisms in a sample of more than 300 unrelated Italian subjects with well-defined geographical origins. We combined several analytical approaches to interpret genome-wide data on 1272 individuals from European, Middle Eastern, and North African populations. We detected three major ancestral components contributing different proportions across the Italian peninsula, and signatures of continuous gene flow within Italy, which have produced remarkable genetic variability among contemporary Italians. In addition, we have extracted novel details about the Italian population’s ancestry, identifying the genetic signatures of major historical events in Europe and the Mediterranean basin from the Neolithic (e.g., peopling of Sardinia) to recent times (e.g., ‘barbarian invasion’ of Northern and Central Italy). These results are valuable for further genetic, epidemiological and forensic studies in Italy and in Europe."
I really love no information abstracts, don't you?
This is the link to the Supplementary Info:
http://www.nature.com/ejhg/journal/...g/journal/vaop/ncurrent/abs/ejhg2015233a.html
I've gone through it all and I have some thoughts, but it's too late to get into it now. I'll just say that although it's better than the Busby effort, some of the choices are still obscure to me, and at least in the supplement there is no clarity as to the direction of the gene flow. Maybe if I can get my hands on the actual paper it will seem clearer, but I also get the feeling, as I did with the Busby paper, that I'm back to a time five years or more in the past before Lazaridis et al or Haak et al and Allentoft et al.
To get started, nothing really new on the PCA front except that Armenians are so removed from other Near Easterners. Turks as well to a certain extent. :
There's also a graphic on Italian variation. The general cline is as expected, except that Calabrians (Reggio Calabria) are south of some of the Sicilians. That may have to do with the samples chosen for Sicily, which are Trapani and Ragusa. I doubt that there'd be much difference between Reggio and, say, Messina, but some Sicilian posters might know better. Also, there are some samples floating out of the expected cline in north and central Italy. This may have to do with the fact that there has been a certain amount of intermarriage across provincial lines in northern and central Italy starting around the end of the 19th century. I can't see anything in the supplement as to their standards for sample inclusion. Not that it would make much difference, but I don't know why they would have chosen Ferrara for Emilia Romagna.
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