I did not report Joe's results in my re-analysis of the Genomes Unzipped data, as his confidence interval intersected 0. For the record, his sample, like that Vincent Plagnol, didn't show any of the "yellow" cluster that was shared by Arabs and Dan Vorhaus (an Ashkenazi Jew).
Joe's explanation that his anomalous results is due to similar allelic frequencies in some markers between Ashkenazi Jews and southern Europeans is quite interesting, and it is based on a dissection of the markers used by EURO-DNA-CALC.
As I stated in my reanalysis of Plagnol's data, his result might also be due to:
a European-origin component in the composite Ashkenazi Jewish gene pool that he happens to share.
Joe's discovery about similar allele frequencies in some markers between Ashkenazi Jews and Italians is quite interesting in terms of my theory about the origin of the European component in the Ashkenazi Jewish gene pool.
Some early studies on AJ, using Y-chromosomes (pdf) overestimated their Near Eastern component by considering them a mix between Levantine and north/central European populations. But, this made the assumption that Jewish ancestors took a Lufthansa flight to Germany rather than spend 1,000+ years in the territory of the Roman Empire and the Hellenistic world where there might also have been introgression of European elements into their gene pool.
Thus, it may very well be that Ashkenazi Jews are distinctive with respect to NW Europeans both in terms to an ancient Near Eastern ancestry (shared with Arabs and "discovered" in my re-analysis) and with respect to Southern European ancestry corresponding to particular populations they interacted with during their sojourn in the Roman Empire.
To conclude, the release of the Genomes Unzipped data on the web has been beneficial to all involved: a few bloggers like myself could run and test their tools on the data, and people like Joe could give feedback on these tools. This is a strong argument in favor of open source tools and public available data and against the use of proprietary databases/ancestry estimation methods/datasets barricaded behind various controls.
As I continue my various ADMIXTURE-experiments, I will be sure to revisit the Genomes Unzipped folk and all those who wish to join them.
UPDATE (Oct 23): A much more detailed analysis of Genomes Unzipped individuals.
UPDATE (Nov 1): Joe Pickrell discovers Jewish great-grandparent