November 30, 2010

Cluster galore: re-analysis of Behar et al. (2010) data

I have re-analyzed the data of Behar et al. (2010) using my Clusters Galore method. See my previous post on the HGDP panel for some technical details.

Here are the 47 clusters of the optimal mclust solution over the MDS representation retaining 26 dimensions:

Each row has the number of individuals who are mapped to each of the 47 clusters. Here are a few comments:

The discovery that Jewish populations can be subdivided into numerous clusters is not inconsistent with Behar et al. (2010) and their observation of the existence of three major clusters in Jewish populations. This is a difference of detail.

Most clusters strongly map to single populations; many populations with "tribal" traditions and high levels of sanguinity are split into multiple clusters, suggesting the existence of sub-structure in them. And, there are a few clusters spanning several populations, such as #1 (Balto-Slavic), #22 (Syrians-Jordanians-Lebanese), #29 (Ethiopians and Ethiopian Jews), #25 (Romanians and Hungarians), #31 (Iranian and Iraqi Jews).


horacioh said...

Pre-A.J. belonged at one of the three nucleous of Jewish ancient populations, that evolving the called "Syrian-European
nucleous" (Greek and Roman times of profuse and lavish
proselytism with genetic inlays).
The "Babilonian and Persian nucleous" and "The Coptic nucleus" are the others of these three Ancient centers.
The A.J. Europeans Components (around 35 to 50%), are, a half from South Europe acquired in ancient times, while the named “Hellenistic Proselytism” in Greek, Anatolia and Rome including Women and Men (“mtDNA” and “Y” markers) as well.
The other half: a 1/4 of the Whole DNA markers was shared and inlaying with E. Europe and host populations along the Galut or Diaspora life. The other 1/4 part was mainly from converted women and it could be seen in the mtDNA almost exclusively.
The W.A. markers represents the time when A. J. were living in E. Europe and the contact with Turkish Jews Khazars – a mixed Jews
people with West and Central Asia ancient components and I call "Medieval Age Four Nucleus East Europe" - and the inbred
into religious restrictions in Middle Ages, and Modern Era, that was the norm, modifying the profile patterns from a “Coptic” - “European Syrian” Jewish ancient mix returning and resulting take in part to a more "South East European Syrian like".
The A.J. hyperhaploydia and heterozygosis, - practically almost absent in Sephardic - as well a great L.D. that could cluster these A.J. populations everywhere you want (not common in isolated population, also for mtDNA coming in great rate from host population, and endogamy practice that Ashkenazim hold) is explained easily..
Other from "Ethiopian mtDNA Heritage: Tracking Gene Flow Across and Around the Gate of Tears" - Red Sea - . Am. J. Hum. Genet.2004 Toomas Kivisild, et al
“In this respect, Ethiopians differ explicitly from most other sub-Saharan African populations studied thus far.Within Ethiopia, the frequency of "N" lineages is significantly higher (P > .05) in samples that originate from its northern territory (48%), which was the center of the Aksum kingdom, than among other Ethiopians.. At the same time, there was no significant difference in the proportions of haplogroup "N" between the Semitic and Cushitic linguistic groups in our sample—for example,between Amharas and Oromos.” This includes Ethiopian Jews.
“On the other hand,.. the rise of Semitic cultural influence in the region Hence, Ethiopians may have been recipients of the southern Arabian J1- M267 chromosomes but have not been efficient donors of the E3b1- M78 chromosomes to southern Arabia -low or absent % there-, although East Africans may have carried the latter to Egypt and, farther, to Europe via the Levantine corridor.”
“HVS-I mtDNA haplotype 16126-16305T-16362 that occurs(12.5%)in Ethiopian Jews (Thomas et al. 2002). Their elevated frequency
and uniform presence among major language groups in Ethiopia (table 1) suggests that these derived
lineages may represent a relatively old introgression of
lineages to the Ethiopian mtDNA pool from the N.E.”
Note also that now Ashkenazim have 24% of E3b1, more than Sephardim 19%-20%.
“East African Y chromosomes in haplogroup E3b1-M78 which is abundant (38%), and may have originated in Ethiopia (Cruciani et al. 2004; Luis et al. 2004). It is interesting that, like E3b1-M78,these mtDNA haplogroups are absent in our Yemeni sample - South Arabia Peninsula - Note that the identified time window is close to the proposed division of the Semitic and Cushitic branches of Afro-Asiatic languages (Militarev 2003) and corresponds broadly to the beginning of deep environmental changes in the deserts of the Sahara and the Arabian Peninsula",in LGM..
"A high proportion of Ethiopian lineages mtDNA "N1a", significantly more abundant in the northeast of that country -48%- trace their w.E. origin in haplogroup N through assorted gene flow at different times and involving different source populations" - Egypt, M.E. etc -

Kate said...

Another interesting fact about human population is that there are about 300 individual models of human psyche according to the Catalog of Human Population lab. This means that there will be approximately 23 million representatives of every human subtype structure in 2011.