The Genetic Background of Ashkenazi Jews
Over at Gene Expression you can read an understandable discussion with neat graphics about the genetic background of Ashkenazi Jews. Some of the conclusions:
1) Jewish populations do have a common ancestral affinity.
2) But, that affinity is complemented by admixture with the populations amongst whom the Diaspora settled.
3) There is a suggestion that in the case of Ashkenazi Jews the European contribution was more likely to be from southern, and not northern, Europe. This is somewhat surprising in light of the fact that the Ashkenazi group crystallized during the medieval period in northern Europe, amongst German and Slavic speaking peoples. These data would imply that in fact there was a relatively strong separation between these groups and the Jews, at least when it came to gene flow into the Jewish group (other data from Poland does show the effect of Jewish assimilation into the gentile majority). Therefore, the admixture may have occurred within the bounds of the former Roman Empire, during the Imperial or early post-Imperial period.
4) The close relationship of Jews to Palestinians is not surprising. Jews are reputedly a Levantine population by origin, and the historical and genetic evidence points to Arabicization in the Levant and Mesopotamia as having occurred through acculturation, and not population replacement. Many of the Palestinians are likely of original Jewish or Samaritan origin, though I would guess that they were likely at least nominally Christianized during the Byzantine persecutions of the 6th century.
5) There remain questions as to which groups the Ashkenazi Jews admixed with, and when they admixed. There should be a different pattern of genetic variance if the admixture event was early and ceased, or if it was constant and gradual gene flow. The phylogenetics implies the former, because of the lack of much allele sharing with northern Europeans specifically, amongst whom the Ashkenazi Jews were resident for the past ~1,000 years. Within the text of the paper there are also hints of possible relationships to a population of the Caucasus, opening an avenue for some validity of the Khazar hypothesis. There have been other data which also point to the Khazar hypothesis. The origins of the Jews then likely are complex.